Pilipinas Total Gas Inc. vs. CIR G.R. No.

207112 December 8, 2015

Counting of the 120 day period

(SC quoted Sec 112(C) Tax Code) From the above, it is apparent that the CIR has 120 days from the
date of submission of complete documents to decide a claim for tax credit or refund of creditable
input taxes. The taxpayer may, within 30 days from receipt of the denial of the claim or after the
expiration of the 120-day period, which is considered a "denial due to inaction," appeal the decision
or unacted claim to the CTA.

To be clear, Section 112 (C) categorically provides that the 120-day period is counted "from the date
of submission of complete documents in support of the application."
Indeed, the 120-day period granted to the CIR to decide the administrative claim under the Section
112 is primarily intended to benefit the taxpayer, to ensure that his claim is decided judiciously and
expeditiously. After all, the sooner the taxpayer successfully processes his refund, the sooner can
such resources be further reinvested to the business translating to greater efficiencies and
productivities that would ultimately uplift the general welfare. To allow the CIR to determine the
completeness of the documents submitted and, thus, dictate the running of the 120-day period,
would undermine these objectives, as it would provide the CIR the unbridled power to indefinitely
delay the administrative claim, which would ultimately prevent the filing of a judicial claim with the
CTA.
Ideally, upon filing his administrative claim, a taxpayer should complete the necessary documents to
support his claim for tax credit or refund or for excess utilized VAT. After all, should the taxpayer
decide to submit additional documents and effectively extend the 120-period, it grants the CIR more
time to decide the claim. Moreover, it would be prejudicial to the interest of a taxpayer to prolong
the period of processing of his application before he may reap the benefits of his claim. Therefore,
ideally, the CIR has a period of 120 days from the date an administrative claim is filed within which
to decide if a claim for tax credit or refund of excess unutilized VAT has merit.

Thus, when the VAT was first introduced through Executive Order No. 273, 32 the pertinent rule was
that:

(e) Period within which refund of input taxes may be made by the Commissioner. The
Commissioner shall refund input taxes within 60 days from the date the application for refund
was filed with him or his duly authorized representative. No refund or input taxes shall be
allowed unless the VAT-registered person files an application for refund within the period
prescribed in paragraphs (a), (b) and (c), as the case may be.

[Emphasis Supplied]

When Republic Act (R.A.) No. 7716 33 was, however, enacted on May 5, 1994, the law was amended
to read:

(d) Period within which refund or tax credit of input taxes shall be made. In proper cases,
The Commissioner shall grant a refund or issue the tax credit for creditable input taxes within
 sixty (60) days from the date of submission of complete documents in support of the application
filed in accordance with sub-paragraphs (a) and (b) hereof. In case of full or partial denial of the
claim for tax refund or tax credit, or the failure on the part of the Commissioner to act on the
application within the period prescribed above, the taxpayer affected may, within thirty (30) days
from the receipt of the decision denying the claim or after the expiration of the sixty-day period,
appeal the decision or the unacted claim with the Court of Tax Appeals.

[Emphasis Supplied]

Again, while the CIR was given only 60 days within which to act upon an administrative claim for
refund or tax credit, the period came to be reckoned "from the date of submission of complete
documents in support of the application." With this amendment, the date when a taxpayer made its
submission of complete documents became relevant.
Then, when the NIRC 34 was enacted on January 1, 1998, the rule was once more amended to read:

(D) Period within which Refund or Tax Credit of Input Taxes shall be Made. In proper
cases, the Commissioner shall grant a refund or issue the tax credit certificate for creditable input
taxes within one hundred twenty (120) days from the date of submission of compete documents
in support of the application filed in accordance with Subsections (A) and (B) hereof.

In case of full or partial denial of the claim for tax refund or tax credit, or the failure on the part
of the Commissioner to act on the application within the period prescribed above, the taxpayer
affected may, within thirty (30) days from the receipt of the decision denying the claim or after
the expiration of the one hundred twenty day-period, appeal the decision or the unacted claim
with the Court of Tax Appeals.

[Emphasis Supplied]

This time, the period granted to the CIR to act upon an administrative claim for refund was extended
to 120 days. The reckoning point however, remained "from the date of submission of complete
documents."

Aware that not all taxpayers were able to file the complete documents to allow the CIR to properly
evaluate an administrative claim for tax credit or refund of creditable input taxes, the CIR issued
RMC No. 49-2003, which provided:

Q-18: For pending claims with incomplete documents, what is the period within which to
submit the supporting documents required by the investigating/processing office? When should
the investigating/processing office officially receive claims for tax credit/refund and what is the
period required to process such claims?

A-18: For pending claims which have not been acted upon by the investigating/processing
office due to incomplete documentation, the taxpayer-claimants are given thirty (30) days
within which to submit the documentary requirements unless given further extension by the
head of the processing unit, but such extension should not exceed thirty (30) days.
 For claims to be filed by claimants with the respective investigating/processing office of the
administrative agency, the same shall be officially received only upon submission of complete
documents.

For current and future claims for tax credit/refund, the same shall be processed within one
hundred twenty (120) days from receipt of the complete documents. If, in the course of the
investigation and processing of the claim, additional documents are required for the proper
determination of the legitimate amount of claim, the taxpayer-claimants shall submit such
documents within thirty (30) days from request of the investigating/processing office, which
shall be construed as within the one hundred twenty (120)-day period.

[Emphases Supplied]

Consequently, upon filing of his application for tax credit or refund for excess creditable input taxes,
the taxpayer-claimant is given thirty (30) days within which to complete the required documents,
unless given further extension by the head of the processing unit. If, in the course of the
investigation and processing of the claim, additional documents are required for the proper
determination of the legitimate amount of claim, the taxpayer-claimants shall submit such
documents within thirty (30) days from request of the investigating/processing office. Notice, by
way of a request from the tax collection authority to produce the complete documents in these
cases, became essential. It is only upon the submission of these documents that the 120-day period
would begin to run.
With the amendments only with respect to its place under Section 112, the Court finds that RMC No.
49-2003 should still be observed. Thus, taking the foregoing changes to the law altogether, it
becomes apparent that, for purposes of determining when the supporting documents have been
completed it is the taxpayer who ultimately determines when complete documents have been
submitted for the purpose of commencing and continuing the running of the 120-day period. After
all, he may have already completed the necessary documents the moment he filed his
administrative claim, in which case, the 120-day period is reckoned from the date of filing. The
taxpayer may have also filed the complete documents on the 30th day from filing of his application,
pursuant to RMC No. 49-2003. He may very well have filed his supporting documents on the first day
he was notified by the BIR of the lack of the necessary documents. In such cases, the 120-day period
is computed from the date the taxpayer is able to submit the complete documents in support of his
application.
To summarize, for the just disposition of the subject controversy, the rule is that from the date an
administrative claim for excess unutilized VAT is filed, a taxpayer has thirty (30) days within which to
submit the documentary requirements sufficient to support his claim, unless given further extension
by the CIR. Then, upon filing by the taxpayer of his complete documents to support his application,
or expiration of the period given, the CIR has 120 days within which to decide the claim for tax credit
or refund. Should the taxpayer, on the date of his filing, manifest that he no longer wishes to submit
any other addition documents to complete his administrative claim, the 120 day period allowed to
the CIR begins to run from the date of filing.
 In all cases, whatever documents a taxpayer intends to file to support his claim must be completed
within the two-year period under Section 112 (A) of the NIRC. The 30-day period from denial of the
claim or from the expiration of the 120-day period within which to appeal the denial or inaction of
the CIR to the CTA must also be respected.

It bears mentioning at this point that the foregoing summation of the rules should only be made
applicable to those claims for tax credit or refund filed prior to June 11, 2014, such as the claim at
bench.

Total Gas Citing San Roque Case

Finally, it should be mentioned that the appeal made by Total Gas to the CTA cannot be said to be
premature on the ground that it did not observe the otherwise mandatory and jurisdictional 120+30 day
period. When Total Gas filed its appeal with the CTA on January 23, 2009, it simply relied on BIR Ruling
No. DA-489-03, which, at that time, was not yet struck down by the Court's ruling in Aichi. As explained
in San Roque, this Court recognized a period in time wherein the 120-day period need not be strictly
observed. Thus:

To repeat, a claim for tax refund or credit, like a claim for tax exemption, is construed strictly
against the taxpayer. One of the conditions for a judicial claim of refund or credit under the VAT
System is compliance with the 120+30 day mandatory and jurisdictional periods. Thus, strict
compliance with the 120+30 day periods is necessary for such a claim to prosper, whether
before, during, or after the effectivity of the Atlas doctrine, except for the period from the
issuance of BIR Ruling No. DA-489-03 on 10 December 2003 to 6 October 2010 when the Aichi
doctrine was adopted, which again reinstated the 120+30 day periods as mandatory and
jurisdictional.

xxx xxx xxx

Clearly, BIR Ruling No. DA-489-03 is a general interpretative rule. Thus, all taxpayers can rely on
BIR Ruling No. DA-489-03 from the time of its issuance on 10 December 2003 up to its reversal by
this Court in Aichi on 6 October 2010, where this Court held that the 120+30 day periods are
mandatory and jurisdictional.

At this stage, a review of the nature of a judicial claim before the CTA is in order. In Atlas
Consolidated Mining and Development Corporation v. CIR, it was ruled

. . . First, a judicial claim for refund or tax credit in the CTA is by no means an original action but
rather an appeal by way of petition for review of a previous, unsuccessful administrative claim.
Therefore, as in every appeal or petition for review, a petitioner has to convince the appellate
court that the quasi-judicial agency a quo did not have any reason to deny its claims. In this case,
it was necessary for petitioner to show the CTA not only that it was entitled under substantive
law to the grant of its claims but also that it satisfied all the documentary and evidentiary
requirements for an administrative claim for refund or tax credit. Second, cases filed in the CTA
are litigated de novo. Thus, a petitioner should prove every minute aspect of its case by
presenting, formally offering and submitting its evidence to the CTA. Since it is crucial for a
petitioner in a judicial claim for refund or tax credit to show that its administrative claim should
 have been granted in the first place, part of the evidence to be submitted to the CTA must
necessarily include whatever is required for the successful prosecution of an administrative
claim. 39

[Underscoring Supplied]

Mindanao II Geothermal Partnership v. CIR G.R. Nos. 193301 & 194637 March 11 2013

Cited by Silicon Philippines Inc. v. CIR G.R. No. 173241 March 25, 2015

Summary of Rules on Prescriptive Periods Involving VAT

We summarize the rules on the determination of the prescriptive period for filing a tax refund or credit
of unutilized input VAT as provided in Section 112 of the 1997 Tax Code, as follows:

(1) An administrative claim must be filed with the CIR within two years after the close of the taxable
quarter when the zero-rated or effectively zero-rated sales were made.

(2) The CIR has 120 days from the date of submission of complete documents in support of the
administrative claim within which to decide whether to grant a refund or issue a tax credit certificate.
The 120-day period may extend beyond the two-year period from the filing of the administrative claim if
the claim is filed in the later part of the two-year period. If the 120-day period expires without any
decision from the CIR, then the administrative claim may be considered to be denied by inaction.

(3) A judicial claim must be filed with the CTA within 30 days from the receipt of the CIR's decision
denying the administrative claim or from the expiration of the 120-day period without any action from
the CIR.

(4) All taxpayers, however, can rely on BIR Ruling No. DA-489-03 from the time of its issuance on 10
December 2003 up to its reversal by this Court in Aichi on 6 October 2010, as an exception to the
mandatory and jurisdictional 120+30 day periods.

CIR v. Visayas Geothermal Power Co., Inc. G.R. No. 181276 November 11, 2013

Therefore, although the 120+30 day period in Section 112 (D) is mandatory and jurisdictional and must
be applied from the effectivity of the 1997 Tax Code on January 1, 1998, an exception shall be made for
judicial claims filed from the issuance of BIR Ruling No. DA 489-03 on December 10, 2003 until the
promulgation of Aichi on October 6, 2010. During the said period, a judicial claim for refund may be filed
with the CTA even before the lapse of the 120-day period given to the BIR to decide on the
administrative case.

In sum, based on the foregoing discussion, the rules for the filing of a claim for refund or tax credit of
unutilized input credit VAT are as follows:

1. The taxpayer has two (2) years after the close of the taxable quarter when the relevant sales
were made within which to file an administrative claim before the CIR for a refund of the creditable
input tax or the issuance of a tax credit certificate, regardless of when the input VAT was paid, according
to Section 112 (A) of the NIRC and Mirant.

2. The CIR is given 120 days, from the date of the submission of the complete documents in
support of the application for tax refund or tax credit, to act on the said application.

3. If the CIR fully or partially denies the application or fails to act on the same within the required
120-day period, the taxpayer is allowed to appeal the decision or inaction of the CIR to the CTA. For this
reason, the taxpayer has 30 days from his receipt of the decision of the CIR or from the lapse of the 120-
day period, within which to file a petition for review with the CTA. In no case shall a petition for review
be filed with the CTA before the expiration of the 120-day period. The judicial claim need not be filed
within the two-year prescriptive period referred to in Section 112 (A), which only pertains to
administrative claims.

4. The two-year period referred to in Section 229 of the NLRC does not apply to appeals filed
before the CTA, in relation to claims for refund or issuance of tax credits made pursuant to Section 112.
Consequently, an appeal may be maintained with the CTA for so long as it observes the abovementioned
period for filing the appeal.

5. Following San Roque the 120+30 day period is mandatory and jurisdictional from January 1,
1998 (the effectivity of the 1997 Tax Code). However, from December 10, 2003 (the date BIR Ruling No.
DA 489-03 was issued) until October 6, 2010 (the promulgation of Aichi), judicial claims need not follow
the 120+30 day period. Thereafter, Aichi shall be the controlling rule for all claims filed with the CTA and
the 120+30 day period must be observed.

CIR v. Dash Engineering Phils Inc. G.R. No. 184145 December 11, 2013

Petitioner is entirely correct in its assertion that compliance with the periods provided for in the
abovequoted provision is indeed mandatory and jurisdictional, as affirmed in this Court's ruling in San
Roque, where the Court En Banc settled the controversy surrounding the application of the 120+30-day
period provided for in Section 112 of the NIRC and reiterated the Aichi doctrine that the 120+30-day
period is mandatory and jurisdictional. Nonetheless, the Court took into account the issuance by the
Bureau of Internal Revenue (BIR) of BIR Ruling No. DA-489-03 which misled taxpayers by explicitly
stating that taxpayers may file a petition for review with the CTA even before the expiration of the 120-
day period given to the CIR to decide the administrative claim for refund. Even though observance of the
periods in Section 112 is compulsory and failure to do so will deprive the CTA of jurisdiction to hear the
case, such a strict application will be made from the effectivity of the Tax Reform Act of 1997 on January
1, 1998 until the present, except for the period from December 10, 2003 (the issuance of the erroneous
BIR ruling) to October 6, 2010 (the promulgation of Aichi), during which taxpayers need not wait for the
lapse of the 120+30-day period before filing their judicial claim for refund. TAECSD
The case at bench, however, does not involve the issue of premature filing of the petition for review
with the CTA. Rather, this petition seeks the denial of DEPI's claim for refund for having been filed late
or after the expiration of the 30-day period from the denial by the CIR or failure of the CIR to make a
decision within 120 days from the submission of the documents in support of respondent's
administrative claim.

In San Roque, one of the respondents similarly filed its petition for review with the CTA well after the
120+30-day period. In denying the taxpayer's claim for refund, this Court explained that: CAaDSI

Unlike San Roque and Taganito, Philex's case is not one of premature filing but of late filing.
Philex did not file any petition with the CTA within the 120-day period. Philex did not also file
any petition with the CTA within 30 days after the expiration of the 120-day period. Philex filed
its judicial claim long after the expiration of the 120-day period, in fact 426 days after the lapse
of the 120-day period. In any event, whether governed by jurisprudence before, during or after
the Atlas case, Philex's judicial claim will have to be rejected because of late filing. Whether the
two-year prescriptive period is counted from the date of payment of the output VAT following
the Atlas doctrine, or from the close of the taxable quarter when the sales attributable to the
input VAT were made following the Mirant and Aichi doctrines, Philex's judicial claim was
indisputably filed late.

The Atlas doctrine cannot save Philex from the late filing of its judicial claim. The inaction of the
Commissioner on Philex's claim during the 120-day period is, by express provision of law,
"deemed a denial" of Philex's claim. Philex had 30 days from the expiration of the 120-day
period to file its judicial claim with the CTA. Philex's failure to do so rendered the "deemed a
denial" decision of the Commissioner final and inappealable. The right to appeal to the CTA
from a decision or "deemed a denial" decision of the Commissioner is merely a statutory
privilege, not a constitutional right. The exercise of such statutory privilege requires strict
compliance with the conditions attached by the statute for its exercise. Philex failed to comply
with the statutory conditions and must thus bear the consequences. 23 (Emphases supplied)

Therefore, in accordance with San Roque, respondent's judicial claim for refund must be denied for
having been filed late. Although respondent filed its administrative claim with the BIR on August 9, 2004
before the expiration of the two-year period in Section 112 (A), it undoubtedly failed to comply with the
120+30-day period in Section 112 (D) (now subparagraph C) which requires that upon the inaction of the
CIR for 120 days after the submission of the documents in support of the claim, the taxpayer has to file
its judicial claim within 30 days after the lapse of the said period. The 120 days granted to the CIR to
decide the case ended on December 7, 2004. Thus, DEPI had 30 days therefrom, or until January 6, 2005,
to file a petition for review with the CTA. Unfortunately, DEPI only sought judicial relief on May 5, 2005
when it belatedly filed its petition to the CTA, despite having had ample time to file the same, almost
four months after the period allowed by law. As a consequence of DEPI's late filing, the CTA did not
properly acquire jurisdiction over the claim.

CIR v. Mindanao II Geothermal Partnership G.R. No. 191498 January 15, 2014
It is worthy to note that in San Roque, this ponente registered her dissent to the retroactive application
of the mandatory and jurisdictional nature of the 120+30 day period provided under Section 112 (D) of
the Tax Code which, in her view, is unfair to taxpayers.1 It has been the view of this ponente that the
mandatory nature of 120+30 day period must be completely applied prospectively or, at the earliest,
only upon the finality of Aichi in order to create stability and consistency in our tax laws. Nevertheless,
this ponente is mindful of the fact that judicial precedents cannot be ignored. Hence, the majority view
expressed in San Roque must be applied.

SUMMARY OF RULES ON PRESCRIPTIVE PERIODS FOR CLAIMING REFUND OR CREDIT OF INPUT VAT

The lessons of this case may be summed up as follows:

A. Two-Year Prescriptive Period

1. It is only the administrative claim that must be filed within the two-year prescriptive period. (Aichi)
2.The proper reckoning date for the two-year prescriptive period is the close of the taxable quarter
when the relevant sales were made. (San Roque)
3. The only other rule is the Atlas ruling, which applied only from 8 June 2007 to 12 September 2008.
Atlas states that the two-year prescriptive period for filing a claim for tax refund or credit of unutilized
input VAT payments should be counted from the date of filing of the VAT return and payment of the tax.
(San Roque)
B. 120+30 Day Period
1. The taxpayer can file an appeal in one of two ways: (1) file the judicial claim within thirty days after
the Commissioner denies the claim within the 120-day period, or (2) file the judicial claim within thirty
days from the expiration of the 120-day period if the Commissioner does not act within the 120-day
period.
2. The 30-day period always applies, whether there is a denial or inaction on the part of the CIR.
3. As a general rule, the 30-day period to appeal is both mandatory and jurisdictional. (Aichi and San
Roque)
4. As an exception to the general rule, premature filing is allowed only if filed between 10 December
2003 and 5 October 2010, when BIR Ruling No. DA-489-03 was still in force. (San Roque)
5. Late filing is absolutely prohibited, even during the time when BIR Ruling No. DA-489-03 was in force.
(San Roque)

CBK Power Co. Ltd vs. CIR G.R. Nos. 198729-30 January 15, 2014

It must be emphasized that this is not a case of premature filing of a judicial claim. Although petitioner
did not file its judicial claim with the CTA prior to the expiration of the 120-day waiting period, it failed
to observe the 30-day prescriptive period to appeal to the CTA counted from the lapse of the 120-day
period.

Petitioner is similarly situated as Philex in the same case, San Roque, 18 in which this Court ruled:
Unlike San Roque and Taganito, Philex's case is not one of premature filing but of late filing.
Philex did not file any petition with the CTA within the 120-day period. Philex did not also file any
petition with the CTA within 30 days after the expiration of the 120-day period. Philex filed its
judicial claim long after the expiration of the 120-day period, in fact 426 days after the lapse of
the 120-day period. In any event, whether governed by jurisprudence before, during, or after the

1
Underscoring Supplied by RDD
 Atlas case, Philex's judicial claim will have to be rejected because of late filing. Whether the two-
year prescriptive period is counted from the date of payment of the output VAT following the
Atlas doctrine, or from the close of the taxable quarter when the sales attributable to the input
VAT were made following the Mirant and Aichi doctrines, Philex's judicial claim was indisputably
filed late.

The Atlas doctrine cannot save Philex from the late filing of its judicial claim. The inaction of the
Commissioner on Philex's claim during the 120-day period is, by express provision of law,
"deemed a denial" of Philex's claim. Philex had 30 days from the expiration of the 120-day period
to file its judicial claim with the CTA. Philex's failure to do so rendered the "deemed a denial"
decision of the Commissioner final and inappealable. The right to appeal to the CTA from a
decision or "deemed a denial" decision of the Commissioner is merely a statutory privilege, not a
constitutional right. The exercise of such statutory privilege requires strict compliance with the
conditions attached by the statute for its exercise. Philex failed to comply with the statutory
conditions and must thus bear the consequences. (Emphases in the original)

Likewise, while petitioner filed its administrative and judicial claims during the period of applicability of
BIR Ruling No. DA-489-03, it cannot claim the benefit of the exception period as it did not file its judicial
claim prematurely, but did so long after the lapse of the 30-day period following the expiration of the
120-day period. Again, BIR Ruling No. DA-489-03 allowed premature filing of a judicial claim, which
means non-exhaustion of the 120-day period for the Commissioner to act on an administrative claim, 19
but not its late filing.

As this Court enunciated in San Roque, petitioner cannot rely on Atlas either, since the latter case was
promulgated only on 8 June 2007. Moreover, the doctrine in Atlas which reckons the two-year period
from the date of filing of the return and payment of the tax, does not interpret expressly or impliedly
the 120+30 day periods. 20 Simply stated, Atlas referred only to the reckoning of the prescriptive
period for filing an administrative claim.

For failure of petitioner to comply with the 120+30 day mandatory and jurisdictional period, petitioner
lost its right to claim a refund or credit of its alleged excess input VAT.

With regard to petitioner's argument that Aichi should not be applied retroactively, we reiterate that
even without that ruling, the law is explicit on the mandatory and jurisdictional nature of the 120+30
day period.

Silicon Philippines, Inc. v. CIR G.R. Nos. 184360, 184361 & 184384 February 19, 2014
However, Silicon failed to file an appeal within 30 days from the lapse of the 120-day period, and it only
filed its petition for review with the CTA on March 30, 2001 which was 451 days late. Thus, in
consonance with our ruling in Philex in the San Roque ponencia, Silicon's judicial claim for tax credit or
refund should have been dismissed for having been filed late. The CTA did not acquire jurisdiction over
the petition for review filed by Silicon.

Similarly, Silicon's claim for tax refund for the second quarter of 2000 should have been dismissed for
having been filed out of time. Records show that Silicon filed its claim for tax credit or refund on August
10, 2000. The CIR then had 120 days or until December 8, 2000 to grant or deny the claim. With the
inaction of the CIR to decide on the claim which was deemed a denial of the claim for tax credit or
refund, Silicon had until January 7, 2001 or 30 days from December 8, 2000 to file its petition for review
with the CTA. However, Silicon again failed to comply with the 120+30 day period provided under
Section 112 (C) since it filed its judicial claim only on June 28, 2002 or 536 days late. Thus, the petition
for review, which was belatedly filed, should have been dismissed by the CTA which acquired no
jurisdiction to act on the petition.

Courts are bound by prior decisions. Thus, once a case has been decided one way, courts have no choice
but to resolve subsequent cases involving the same issue in the same manner.

As this Court has repeatedly emphasized, a tax credit or refund, like tax exemption, is strictly construed
against the taxpayer. The taxpayer claiming the tax credit or refund has the burden of proving that he is
entitled to the refund by showing that he has strictly complied with the conditions for the grant of the
tax refund or credit. Strict compliance with the mandatory and jurisdictional conditions prescribed by
law to claim such tax refund or credit is essential and necessary for such claim to prosper.

Noncompliance with the mandatory periods, nonobservance of the prescriptive periods, and
nonadherence to exhaustion of administrative remedies bar a taxpayer's claim for tax refund or credit,
whether or not the CIR questions the numerical correctness of the claim of the taxpayer. 38 For failure
of Silicon to comply with the provisions of Section 112 (C) of the NIRC, its judicial claims for tax refund or
credit should have been dismissed by the CTA for lack of jurisdiction.

Visayas Geothermal Power Co. vs. CIR G.R. No. 197525 June 4, 2014
CIR not estopped

The petitioner's argument that the CIR should have been estopped from questioning the jurisdiction of
the CTA after actively participating in the proceedings before the CTA Second Division deserves scant
consideration.

It is a well-settled rule that the government cannot be estopped by the mistakes, errors or omissions of
its agents. It has been specifically held that estoppel does not apply to the government, especially on
matters of taxation. Taxes are the nation's lifeblood through which government agencies continue to
operate and with which the State discharges its functions for the welfare of its constituents. Thus, the
government cannot be estopped from collecting taxes by the mistake, negligence, or omission of its
agents. Upon taxation depends the ability of the government to serve the people for whose benefit
taxes are collected. To safeguard such interest, neglect or omission of government officials entrusted
with the collection of taxes should not be allowed to bring harm or detriment to the people.

Rules on claims for refund or tax credit of unutilized input VAT

For clarity and guidance, the Court deems it proper to outline the rules laid down in San Roque with
regard to claims for refund or tax credit of unutilized creditable input VAT. They are as follows:
1. When to file an administrative claim with the CIR:
a. General rule Section 112 (A) and Mirant
Within 2 years from the close of the taxable quarter when the sales were made.
b. Exception Atlas
Within 2 years from the date of payment of the output VAT, if the administrative claim was filed
from June 8, 2007 (promulgation of Atlas) to September 12, 2008 (promulgation of Mirant).
2. When to file a judicial claim with the CTA:
a. General rule Section 112 (D); not Section 229
i. Within 30 days from the full or partial denial of the administrative claim by the CIR; or
ii. Within 30 days from the expiration of the 120-day period provided to the CIR to decide on the
claim. This is mandatory and jurisdictional beginning January 1, 1998 (effectivity of 1997 NIRC).
b. Exception BIR Ruling No. DA-489-03
The judicial claim need not await the expiration of the 120-day period, if such was filed from
December 10, 2003 (issuance of BIR Ruling No. DA-489-03) to October 6, 2010 (promulgation of Aichi).

San Roque Power Corp. vs. CIR G.R. No. 205543 June 30, 2014
For the Court, there is no more point in considering the amended administrative claims for the first and
second quarters of 2006. The amended administrative claims were filed on March 10, 2008 after the
120+30 day periods for filing the judicial claims, counting from the date of filing of the original
administrative claims for the first and second quarters of 2006, had already expired on September 8,
2007 and December 7, 2007, respectively. Taking cognizance of the amended administrative claims in
such a situation would result in the revival of judicial claims that had already prescribed.

Meanwhile, San Roque filed its amended administrative claims for the third and fourth quarters of 2006
on September 21, 2007, before the end of the 120-day period for the CIR to decide on the original
administrative claims for the same taxable quarters. Nonetheless, even if the Court counts the 120+30
day periods from the date of filing of said amended administrative claims, the judicial claims of San
Roque would still be belatedly filed.

Xxx xxx xxx

Unable to contest the belated filing of its judicial claims, San Roque argues against the supposedly
retroactive application of Aichi and the strict observance of the 120+30 day periods.

As the CTA en banc held, Aichi was not applied retroactively to San Roque in the instant case. The
120+30 day periods have already been prescribed under Section 112(C) of the NIRC of 1997, as
amended, when San Roque filed its administrative and judicial claims for refund or tax credit of its
creditable input taxes for the four quarters of 2006. The Court highlights the pronouncement in San
Roque (2013) that strict compliance with the 120+30 day periods is necessary for the judicial claim to
prosper, except for the period from the issuance of BIR Ruling No. DA-489-03 on December 10, 2003 to
October 6, 2010 when Aichi was promulgated, which again reinstated the 120+30 day periods as
mandatory and jurisdictional.

It is still necessary for the Court to explain herein how BIR Ruling No. DA-489-03 is an exception to the
strict observance of the 120+30 day periods for judicial claims. BIR Ruling No. DA-489-03 affected only
the 120-day period as the BIR held therein that "a taxpayer-claimant need not wait for the lapse of the
120-day period before it could seek judicial relief with the CTA by way of Petition for Review. Neither is
it required that the Commissioner should first act on the claim of a particular taxpayer before the CTA
may acquire jurisdiction, particularly if the claim is about to prescribe." Consequently, BIR Ruling No. DA-
489-03 may only be invoked by taxpayers who relied on the same and prematurely filed their judicial
claims before the expiration of the 120-day period for the CIR to act on their administrative claims,
provided that the taxpayers filed such judicial claims from December 10, 2003 to October 6, 2010. BIR
Ruling No. DA-489-03 did not touch upon the 30-day prescriptive period for filing an appeal with the CTA
and cannot be cited by taxpayers, such as San Roque, who belatedly filed their judicial claims more than
30 days after receipt of the adverse decision of the CIR on their administrative claims or the lapse of 120
days without the CIR acting on their administrative claims.
Xxx xxx xxx

Based on the foregoing, "prospective application" of Aichi and Mirant, in the context of San Roque
(2013), only meant that the rulings in said cases would not retroactively affect taxpayers who relied on
Atlas and/or DA-489-03 when they filed their administrative and judicial claims for refund or tax credit
of creditable input taxes during the period when Atlas and DA-489-03 were still in effect. Aichi and
Mirant can still be applied to cases involving administrative and judicial claims filed prior to the
promulgation of said cases and outside the period of effectivity of Atlas and DA-489-03, such as the
instant case.

Cargill Philippines v. CIR G.R. No. 203774 March 11, 2015 (PREMATURE FILING)
The quoted italicized paragraph was also cited by
CBK Power Co. Limited v. CIR G.R. No. 198928 December 3, 2014
Mindanao II Geothermal Partnership v. CIR G.R. No. 204745
Panay Power Corp. v. CIR G.R. No. 203351 January 21, 2015
In the more recent case of Taganito Mining Corporation v. CIR, 41 the Court reconciled the
pronouncements in Aichi and San Roque, holding that from December 10, 2003 to October 6, 2010
which refers to the interregnum when BIR Ruling No. DA-489-03 was issued until the date of
promulgation of Aichi, taxpayer-claimants need not observe the stringent 120-day period; but before
and after said window period, the mandatory and jurisdictional nature of the 120-day period remained
in force, viz.:
Reconciling the pronouncements in the Aichi and San Roque cases, the rule must therefore be that
during the period December 10, 2003 (when BIR Ruling No. DA-489-03 was issued) to October 6,
2010 (when the Aichi case was promulgated), taxpayers-claimants need not observe the 120-day
period before it could file a judicial claim for refund of excess input VAT before the CTA. Before
and after the aforementioned period (i.e., December 10, 2003 to October 6, 2010), the
observance of the 120-day period is mandatory and jurisdictional to the filing of such claim.
(Emphases and underscoring supplied)

Northern Mindanao Power Corp. vs. CIR G.R. No. 185115 February 18 2015 (LATE FILING)
Counting 120 days from 20 June 2000, the CIR had until 18 October 2000 within which to decide on the
claim of petitioner for an input VAT refund attributable to its zero-rated sales for the period covering the
3rd and the 4th quarters of taxable year 1999. If after the expiration of that period respondent still
failed to act on the administrative claim, petitioner could elevate the matter to the court within 30 days
or until 17 November 2000.

Petitioner belatedly filed its judicial claim with the CTA on 28 September 2001. Just like in Philex, this
was a case of late filing. The Court explained thus:

Unlike San Roque and Taganito, Philex's case is not one of premature filing but of late filing.
Philex did not file any petition with the CTA within the 120-day period. Philex did not also file any
petition with the CTA within 30 days after the expiration of the 120-day period. Philex filed its
judicial claim long after the expiration of the 120-day period, in fact 426 days after the lapse of
the 120-day period. In any event, whether governed by jurisprudence before, during, or after the
Atlas case, Philex's judicial claim will have to be rejected because of late filing. Whether the two-
year prescriptive period is counted from the date of payment of the output VAT following the
Atlas doctrine, or from the close of the taxable quarter when the sales attributable to the input
 VAT were made following the Mirant and Aichi doctrines, Philex's judicial claim was indisputably
filed late.
The Atlas doctrine cannot save Philex from the late filing of its judicial claim. The inaction of the
Commissioner on Philex's claim during the 120-day period is, by express provision of law,
"deemed a denial" of Philex's claim. Philex had 30 days from the expiration of the 120-day period
to file its judicial claim with the CTA. Philex's failure to do so rendered the "deemed a denial"
decision of the Commissioner final and inappealable. The right to appeal to the CTA from a
decision or "deemed a denial" decision of the Commissioner is merely a statutory privilege, not a
constitutional right. The exercise of such statutory privilege requires strict compliance with the
conditions attached by the statute for its exercise. Philex failed to comply with the statutory
conditions and must thus bear the consequences.
xxx xxx xxx
Philex's situation is not a case of premature filing of its judicial claim but of late filing, indeed very
late filing. BIR Ruling No. DA-489-03 allowed premature filing of a judicial claim, which means
non-exhaustion of the 120-day period for the Commissioner to act on an administrative claim.
Philex cannot claim the benefit of BIR Ruling No. DA-489-03 because Philex did not file its judicial
claim prematurely but filed it long after the lapse of the 30-day period following the expiration
of the 120-day period. In fact, Philex filed its judicial claim 426 days after the lapse of the 30-day
period. 13 (Emphasis in the original)

Petitioner's claim for the 3rd and the 4th quarters of taxable year 1999 was filed 319 days after the
expiration of the 30-day period. To reiterate, the right to appeal is a mere statutory privilege that
requires strict compliance with the conditions attached by the statute for its exercise. Like Philex,
petitioner failed to comply with the statutory conditions and must therefore bear the consequences. It
already lost its right to claim a refund or credit of its alleged excess input VAT attributable to zero-rated
or effectively zero-rated sales for the 3rd and the 4th quarters of taxable year 1999 by virtue of its own
failure to observe the prescriptive periods.