President CANNOT revoke amnesty but...

Can the incumbent President revoke the amnesty proclamation issued by a former President and concurred in by Congress?

No. Amnesty proclamation issued by a former President under express authority of the Constitution and concurred in by Congress has the nature, force, effect, and operation of a law (People vs. Macadaeg, G.R. No. L-4316, May 28, 1952). Hence, an incumbent president cannot unilaterally revoke the bilateral acts of the former President and Congress in making an amnesty proclamation. Same as a law, amnesty proclamation can only revoke by concurrent actions of the President and Congress. Moreover, amnesty extinguishes the criminal liability of the amnesty beneficiary. Hence, revocation made after the criminal extinction will not prejudice the amnesty beneficiary.

Can the incumbent President nullify the decision of the Department of National Defense for failure to file application for amnesty as an express precondition to the granting of the benefit under an amnesty proclamation and failure to admit his guilt?

Yes. The Department of National Defense is under the control power of the President. Hence, he can nullify its decision granting amnesty benefit despite of the failure of the beneficiary to comply with conditions of the amnesty proclamation. But the nullification is subject to the judicial review. If the court finds that amnesty beneficiary made an application and admitted his guilt therein and the Department of National Defense properly approved the application, it may reverse the decision of the President on the ground of grave abuse of discretion tantamount to lack or in excess of jurisdiction. The proper approval of the amnesty application extinguishes the criminal liability of the applicant for the crime covered by the proclamation.

SOURCE: Short Reviewer on Amnesty for 2018 Bar Exams by Judge Marlo Campanilla; Marlo Campanilla on Facebook; Sunday, September 9, 2018;