Rohm Apollo Semiconductor Philippines vs. Commissioner of Internal Revenue

The 30‑day period for filing a judicial claim for refund or credit of unutilized input VAT with the Court of Tax Appeals, counted from the expiration of the 120‑day waiting period for the Commissioner of Internal Revenue to act or from receipt of the denial, is mandatory and jurisdictional. Failure to file within that period deprives the CTA of jurisdiction over the claim. The exception established in Commissioner of Internal Revenue v. San Roque Power Corporation — permitting premature filing during the effectivity of BIR Ruling No. DA‑489‑03 (10 December 2003 to 5 October 2010) — does not extend to instances of late filing, which are absolutely prohibited even during that window.

Rohm Apollo Semiconductor Philippines, Inc., a domestic corporation registered as an Ecozone Export Enterprise and a VAT taxpayer, engaged Shimizu Philippine Contractors, Inc. to construct a factory in Carmona, Cavite. In July and August 2000, before commercial operations began, Rohm Apollo made initial payments totaling ₱330,919,807.86 for the construction services, treating them as purchases of capital goods. The input VAT paid on those purchases amounted to ₱30,359,615.40 and remained unutilized because the company had yet to generate output VAT.

• Corporate Profile and Registration: Rohm Apollo Semiconductor Philippines, Inc. was a domestic corporation registered with the Securities and Exchange Commission, the Philippine Economic Zone Authority as an Ecozone Export Enterprise, and the Bureau of Internal Revenue as a VAT taxpayer. It manufactured semiconductor products at the People’s Technology Complex — Special Economic Zone in Carmona, Cavite.

• Transaction and Input Tax: In June 2000, prior to commencing commercial operations on 1 September 2001, Rohm Apollo contracted Shimizu Philippine Contractors, Inc. for the construction of a factory. Initial payments were made on 7 July 2000 (₱198,551,884.28) and 3 August 2000 (₱132,367,923.58). The taxpayer treated these payments as purchases of capital goods, giving rise to creditable input VAT of ₱30,359,615.40.

• Administrative Claim and Inaction: On 11 December 2000, Rohm Apollo filed an administrative claim for refund or issuance of a tax credit certificate for the unutilized input VAT. The close of the taxable quarter in which the purchases were made was 30 September 2000; thus the administrative claim fell well within the two‑year prescriptive period under Sections 112(A) and (B) of the 1997 Tax Code. Pursuant to Section 112(D), the Commissioner of Internal Revenue had 120 days from 11 December 2000, or until 10 April 2001, to act on the claim. The Commissioner did not act within that period.

• Judicial Claim Filed Beyond 30‑Day Period: Instead of filing a judicial claim within 30 days from the lapse of the 120‑day period (i.e., by 10 May 2001), Rohm Apollo filed its Petition for Review with the CTA only on 11 September 2002. The taxpayer operated under the belief that a judicial claim had to be filed solely within the two‑year prescriptive period ending on 30 September 2002, and that the 30‑day period in Section 112(D) did not apply to cases of the Commissioner’s inaction.

• CTA Proceedings: The CTA First Division denied the claim on the merits for failure to present VAT returns for the third quarter of 2001 and succeeding quarters, rendering it impossible to determine whether the input taxes had been carried over or utilized. The CTA En Banc affirmed on the same ground.

• Validity of Refund Claim: Rohm Apollo argued that it had satisfied all the legal requirements for a valid claim for refund or tax credit of unutilized input VAT on capital goods under Sections 112(A) and (B) of the 1997 Tax Code.
• Timeliness of Judicial Claim: Petitioner maintained that the judicial claim was timely filed because the only time limit for bringing a judicial claim was the two‑year prescriptive period after the close of the taxable quarter when the purchase was made. It contended that the 30‑day period under Section 112(D) applied only where the Commissioner expressly denied the claim, not where the claim remained unacted upon.

• Jurisdictional Bar — Late Filing: The Commissioner of Internal Revenue contended that the judicial claim was filed beyond the mandatory 30‑day period following the expiration of the 120‑day waiting period, thereby depriving the CTA of jurisdiction over the refund claim. The judicial claim should have been filed by 10 May 2001, but it was brought only on 11 September 2002.

• Timeliness and Jurisdiction: Whether the judicial claim for refund or credit of unutilized input VAT was timely filed within the mandatory 30‑day period after the Commissioner’s inaction, thereby vesting the Court of Tax Appeals with jurisdiction over the claim.

• Timeliness and Jurisdiction: The judicial claim was filed out of time, and the CTA never acquired jurisdiction. Section 112(D) of the 1997 Tax Code establishes two cumulative periods: a 120‑day waiting period for the Commissioner to act on the administrative claim, and a 30‑day period from the receipt of a denial or from the expiration of the 120‑day period within which to appeal to the CTA. The 30‑day period is mandatory and jurisdictional. When the Commissioner fails to act within the 120‑day period, the inaction is deemed a denial, and the taxpayer must file the judicial claim within 30 days thereafter. This rule, settled in Commissioner of Internal Revenue v. San Roque Power Corporation, applies whether the Commissioner issues an express denial or remains silent. Rohm Apollo’s belief that the 30‑day period did not attach to cases of inaction was directly contrary to San Roque, which explained that the 30‑day period was adopted precisely to do away with the old rule that allowed a taxpayer to wait until the two‑year prescriptive period was about to expire. The taxpayer’s administrative claim was filed on 11 December 2000; the 120‑day period lapsed on 10 April 2001. The 30‑day appeal period ended on 10 May 2001. The judicial claim was brought only on 11 September 2002, long after the deadline.

The sole exception to the mandatory and jurisdictional character of the 30‑day period — BIR Ruling No. DA‑489‑03 — could not aid the taxpayer. That ruling, effective from 10 December 2003 to 5 October 2010, permitted premature filing of a judicial claim without waiting for the lapse of the 120‑day period. The Supreme Court in San Roque clarified that the exception covers only premature filing, not late filing. Because Rohm Apollo’s judicial claim was filed on 11 September 2002 — before the BIR ruling was even issued — the taxpayer could not invoke it. Moreover, the claim was indisputably one of late filing, not premature filing. The case therefore fell under the general rule that strict compliance with the 120+30‑day mandatory and jurisdictional periods is required for a judicial claim to prosper. The CTA lost jurisdiction, rendering any discussion of the merits unnecessary.

• Mandatory and Jurisdictional 120+30‑Day Periods — Under Section 112(D) of the 1997 Tax Code, the 120‑day period for the Commissioner to decide an administrative claim for refund or credit of input VAT and the 30‑day period to appeal to the CTA are both mandatory and jurisdictional. Non‑compliance deprives the CTA of jurisdiction over the judicial claim. The taxpayer must file the judicial claim: (a) within 30 days from receipt of the Commissioner’s denial, if the denial is made within the 120‑day period; or (b) within 30 days from the expiration of the 120‑day period, if the Commissioner does not act at all. The old rule that permitted filing a judicial claim without waiting for the Commissioner’s decision when the two‑year prescriptive period was about to expire has been superseded by the 30‑day innovation.

• Exception for Premature Filing (BIR Ruling No. DA‑489‑03) — During the effectivity of BIR Ruling No. DA‑489‑03 (10 December 2003 to 5 October 2010), a taxpayer was excused from waiting for the lapse of the 120‑day period and could prematurely file a judicial claim. This exception applies exclusively to premature filings and does not validate late filings. A judicial claim filed after the 30‑day deadline is absolutely barred, even if brought during the period when the BIR ruling was in force.

• Inaction as Denial — The Commissioner’s failure to act on an administrative claim within the 120‑day waiting period is itself the decision — an implied denial. The taxpayer must treat the expiration of that period as an adverse ruling and appeal within 30 days; it cannot wait for a subsequent express decision.

• “The old rule that the taxpayer may file the judicial claim, without waiting for the Commissioner’s decision if the two‑year prescriptive period is about to expire, cannot apply because that rule was adopted before the enactment of the 30‑day period. The 30‑day period was adopted precisely to do away with the old rule, so that under the VAT System the taxpayer will always have 30 days to file the judicial claim even if the Commissioner acts only on the 120th day, or does not act at all during the 120‑day period.” — This passage explains the rationale for the mandatory 30‑day period and why the old practice of waiting until the end of the two‑year period is no longer allowed.

• “As a general rule, the 30‑day period to appeal is both mandatory and jurisdictional. … premature filing is allowed for cases falling during the time when BIR Ruling No. DA‑489‑03 was in force; nevertheless, late filing is absolutely prohibited even for cases falling within that period.” — The statement concisely encapsulates the rule and its exception.

• “The CIR’s inaction is the decision itself. It is already a denial of the refund claim. Thus, the taxpayer must file an appeal within 30 days from the lapse of the 120‑day waiting period.” — The Court’s clear directive on the legal effect of the Commissioner’s silence.

• Commissioner of Internal Revenue v. San Roque Power Corporation, G.R. No. 187485, 12 February 2013, 690 SCRA 336 — The controlling precedent interpreting Section 112(D) of the 1997 Tax Code. It definitively ruled that the 120+30‑day periods are mandatory and jurisdictional, and that the exception for premature filing under BIR Ruling No. DA‑489‑03 does not extend to late filing. The Supreme Court in Rohm Apollo relied entirely on San Roque’s framework to deny the petition.

• Commissioner of Internal Revenue v. Aichi Forging Company of Asia, Inc., G.R. No. 184823, 6 October 2010, 632 SCRA 422 — Cited to clarify that it is only the administrative claim — not the judicial claim — that must be filed within the two‑year prescriptive period under Sections 112(A) and (B) of the 1997 Tax Code.

• Section 112(D), 1997 Tax Code (R.A. No. 8424), renumbered as Section 112(C) by R.A. No. 9337 — The provision mandates that the Commissioner shall grant a refund or issue a tax credit certificate for creditable input taxes within 120 days from submission of complete documents. In case of full or partial denial, or failure to act within that period, the taxpayer may appeal to the CTA within 30 days from receipt of the decision denying the claim or after the expiration of the 120‑day period. The Supreme Court construed the 120‑day and 30‑day periods as mandatory and jurisdictional, and read the inaction as an implied denial that triggers the 30‑day appeal window.

• Sections 112(A) and (B), 1997 Tax Code — These provisions establish the two‑year prescriptive period for filing an administrative claim for refund or credit of unutilized input VAT attributable to zero‑rated sales or capital goods. The decision confirms that this two‑year period applies solely to the administrative claim, not to the judicial claim, which is separately governed by the 30‑day period in Section 112(D).

Associate Justices Teresita J. Leonardo-De Castro, Lucas P. Bersamin, Jose Portugal Perez, and Estela M. Perlas-Bernabe.

N/A — The decision was unanimous.