Under the deal – aimed at combatting militant groups aligned to the Islamic State (IS) in southern Philippines – the rebels abandoned their goal for a separate state in lieu of broader autonomy.

Moro Islamic Liberation Front (MILF) rebel chairman Murad Ebrahim will now lead a group in governing Bangsamoro, a region with over 3.7 million people.

Under the deal, the first group of about 12,000 combatants is expected to be demobilised starting this year.

According to AP, the Philippines, Western governments and guerrillas view Muslim autonomy as a remedy to decades of Muslim secessionist violence, which the IS could exploit to gain a foothold in the region.

“Our enemy during this struggle is not the soldiers. Our enemy is not the government,” AP quoted Murad as saying after assuming leadership of the Bangsamoro Transition Authority as interim chief minister.

Murad added that he and his men would wage a new “jihad” against graft and mismanagement.

In 2016, the Philippine government under Rodrigo Duterte and MILF met in Kuala Lumpur to formally re-launch the implementation phase of the Bangsamoro agreement, which called for self-government of the area.

Then-prime minister Najib Razak also reiterated the country’s commitment to the Bangsamoro peace deal in southern Philippines “for as long as is desired”.

Malaysia had brokered peace talks as a third-party facilitator for the Southern Philippines Peace Process since 2001.

This paved the way for the signing of an agreement on Bangsamoro between the Philippine government and MILF in 2014.

In January this year, the proposal to create a self-administered area for the Muslim-dominated parts of Mindanao was backed by 85% of voters in a landmark referendum.