G.R. No. 104217 - Manila International Airport Authority vs. Commission on Audit

The petition for certiorari was filed under Rule 65 of the Revised Rules of Court by the Manila International Airport Authority (MIAA), a government-owned and controlled corporation tasked with promoting air traffic and related infrastructure, against the Commission on Audit (COA) and several intervenors.
The dispute arose from the disallowance, by the COA, of an excess payment in the amount of P1,215,947.96 for representation and transportation allowances (RATA) granted to MIAA officials and employees for the period July 1989 to June 1990.

Based on the Letter of Implementation (LOI) No. 97—specifically Section 5.4(g)—MIAA had authorized an increase in the RATA benefits of its Department and Division Managers to 40% of their basic salary.
In compliance with Republic Act (R.A.) No. 6758, otherwise known as the “Compensation and Position Classification Act of 1989,” the authority adjusted the RATA for managers for the period covering July 1989 to June 1991, resulting in a total adjustment amount of P1,215,947.96.

On September 12, 1990, the MIAA Resident Auditor issued a Formal Notice of Disallowance, positing that the RATA payment was excessive because it was based on a 40% increment of the basic salary—which, according to the auditor, violated R.A. No. 6758, Corporate Compensation Circular (CCC) No. 10, and COA Memorandum 90-653.
The auditor contended that, under the law, payment should have been computed based on the highest RATA amount being received by the incumbents as of June 30, 1989, thereby implying that the 40% calculation exceeded what was legally permissible.

MIAA and the intervening officials challenged that the LOI No. 97, particularly Section 5(g), had not been repealed by the provisions of R.A. No. 6758, citing legal opinions from the Government Corporate Counsel (Opinions Nos. 68 and 108).
The petitioners argued that LOI No. 97 continued to authorize a RATA of 40% of the basic salary, even after the effectivity of R.A. No. 6758 which, according to them, should be adjusted to reflect the standardized salary rates rather than be limited to the historical maximum as of June 30, 1989.
Conversely, the COA maintained that R.A. No. 6758—with its provisions in Sections 12 and 22—effectively repealed LOI No. 97. It asserted that the continued payment of RATA should be based on the highest amount previously received by the incumbent as of June 30, 1989.
An additional issue raised pertained to whether the respondents’ act of implementing statutory amendments, through executive legislation, usurped the legislative function, thereby violating the constitutional principle of separation of powers.

Whether LOI No. 97, particularly Section 5(g), is inconsistent with and thereby has been repealed by Section 22 (and related provisions) of R.A. No. 6758.
Whether the grant of RATA (and its subsequent adjustments) to the private petitioners after June 30, 1989, should be based on 40% of their basic (or standardized) salary or on the highest amount of RATA received by incumbents as of that cut-off date.
Whether the respondents, by way of executing statutory amendments via executive legislation, have usurped the legislative function, consequently violating the constitutional doctrine on the separation of powers.