G.R. No. 210646 , July 29, 2015.
COMMISSIONER OF INTERNAL REVENUE, Petitioner, vs. AIR LIQUIDE PHILIPPINES, INC., Respondent.

FACTS

Respondent Air Liquide Philippines, Inc. (ALPI), a VAT-registered domestic corporation, filed its Quarterly VAT Return for the 4th quarter of 2007 on January 22, 2008. On December 23, 2009, ALPI filed an application for a tax credit certificate for unutilized input VAT attributable to its transactions with PEZA-registered enterprises. Without awaiting the resolution of this administrative claim or the expiration of the 120-day period prescribed under Section 112(C) of the National Internal Revenue Code (NIRC), ALPI filed a petition for review with the Court of Tax Appeals (CTA) Division on December 29, 2009, only six days later. The CTA Division dismissed the petition for lack of jurisdiction due to ALPI’s failure to observe the compulsory 120-day waiting period. The CTA En Banc reversed this dismissal, citing the doctrine established in the consolidated cases of CIR v. San Roque, which held that taxpayers could rely on BIR Ruling No. DA-489-03 (issued December 10, 2003) and need not wait for the 120-day period before seeking judicial relief, a ruling that was effective until its reversal in CIR v. Aichi on October 6, 2010. Since ALPI filed its judicial claim on December 29, 2009, within this interim period, the CTA En Banc remanded the case for determination on the merits. The Commissioner of Internal Revenue (CIR) petitioned the Supreme Court, arguing that ALPI could not benefit from the San Roque exception because it did not specifically assert or invoke BIR Ruling No. DA-489-03 in its petitions before the CTA.

ISSUE

Whether or not the CTA Division acquired jurisdiction over ALPI’s petition for review despite its premature filing, and specifically, whether ALPI must have expressly invoked BIR Ruling No. DA-489-03 to benefit from its exception to the 120-day waiting rule.

RULING

The Supreme Court ruled that the CTA Division acquired jurisdiction. The petition was denied, and the CTA En Banc’s decision was affirmed. The Court held that BIR Ruling No. DA-489-03 was a general interpretative rule applicable to all taxpayers, not just to a specific one. Therefore, all taxpayers who filed judicial claims for VAT refund or credit within the period from December 10, 2003 (the ruling’s issuance) to October 6, 2010 (its reversal in Aichi) are not required to wait for the lapse of the 120-day period. The Court clarified that there is no need for a taxpayer to specifically allege or invoke BIR Ruling No. DA-489-03 in its petition to benefit from this exception. To require such an invocation would create an unreasonable classification and complicate the doctrine established in San Roque. Since ALPI filed its judicial claim on December 29, 2009, well within the interim period, its filing was not premature. Consequently, the case was remanded to the CTA Division for the proper determination of the refundable or creditable amount.