President Rodrigo Duterte will implement the peace agreement with the Moro Islamic Liberation Front, the country's biggest rebel group, even if he is also pushing for a shift to a federal form of government, his peace adviser said.

But Secretary Jesus Dureza said the federal system could serve as the government's "last card" in establishing a new Bangsamoro territory, a central feature of the peace agreement signed with former President Benigno Aquino III in 2014.

"Importante na may implemention itong agreement na 'to," Dureza told reporters after the turnover ceremonies at the Office of the Presidential Adviser on the Peace Process in Pasig City.

"We'd like to see an early implementation of these peace agreements that have been signed."

Dureza, who replaced Teresita Deles and returned to his old post, said Duterte could appoint new members of the Bangsamoro Transition Commission, which could draft a new Bangsamoro law.

But Dureza said Malacañang also could not stop congressmen from refiling the old Bangsamoro Basic Law, which languished in the previous Congress over questions on its constitutionality.