G.R. Nos. 255470-71 - COMMISSIONER OF INTERNAL REVENUE, VS. CARGILL PHILIPPINES, INC..D E C I S I O N - Supreme Court E-Library

Ruling

Accordingly, once the administrative claim is filed within the two (2)-year prescriptive period, the taxpayer-claimant must wait for the lapse of the 120-day period and. thereafter, he has a 30-day period within which to file his judicial claim before the CTA, even if said 120-day and 30-day periods would exceed the aforementioned two (2)-year prescriptive period. Nevertheless, the Court in the case of CIR v. San Roque Power Corporation (San Roque) , recognized an exception to the mandatory and jurisdictional nature of the 120-day period . San Roque enunciated that BIR Ruling No. DA-489-03 dated December 10, 2003 , which expressly declared that the "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." provided a valid claim for equitable estoppel under Section 246 of the NIRC. In the more recent case of Taganito Mining Corporation v. CIR , 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[.] x x x x x x In this case, records disclose that anent [respondent's] first refund claim, it filed its administrative claim with the BIR on June 27, 2003, and its judicial claim before the CTA on June 30, 2003, or before the period when BIR Ruling No. DA-489-03 was in effect , i.e. , from December 10, 2003 to October 6, 2010. As such, it was incumbent upon [respondent] to wait for the lapse of the 120-day period before seeking relief with the CTA, and considering that its judicial claim was filed only after three (3) days later, the CIA En Banc , thus, correctly dismissed [respondent's] petition in CTA Case No. 6714 for being prematurely filed. In contrast, records show that with respect to [respondent's] second refund claim, its administrative and judicial claims were both filed on May 31, 2005, or during the period of effectivity of BIR Ruling No. DA-489-03 , and, thus, fell within the exemption window period contemplated in San Roque, i.e. , when taxpayer-claimants need not wait for the expiration of the 120-day period before seeking judicial relief. Verily, the CTA En Banc erred when it outrightly dismissed CTA Case No. 7262 on the ground of prematurity. This notwithstanding, the Court finds that [respondent's] second refund claim in the amount of PHP 22,194,446.67 which allegedly represented unutilized input VAT covering the period March 1, 2003 to August 31, 2004 should not be instantly granted. This is because the determination of [respondent's] entitlement to such claim, if any, would necessarily involve factual issues and, thus, are evidentiary in nature which are beyond the pale of judicia