The Philippines on Saturday restarted peace talks with the country's largest Muslim rebel group, the first under President Rodrigo Duterte aimed at ending decades of violence that has claimed tens of thousands of lives.

Negotiators for the two sides said the weekend talks in Malaysia would discuss details of Duterte's peace road map.

"They will discuss the road map to clarify certain issues. But let me warn everyone, it is not an easy task. It is very complicated," Jesus Dureza, presidential adviser on the peace process, told reporters in Kuala Lumpur without elaborating.

The 12,000-strong Moro Islamic Liberation Front (MILF) has waged a bloody insurgency in the mainly Muslim southern Philippines since the 1970s but an accord signed in 2014 had raised hopes of a lasting peace.

Under the accord, the rebels would have only given up their arms after a law was passed creating an autonomous homeland in Mindanao and a regional government was elected.

The vote was meant to take place alongside the May 2016 general election.

However a bungled raid into MILF territory that killed 44 police commandos in 2015 helped derail the passage of the law and stalled the peace process with the rebels.

Dureza described the relaunching of the talks in Malaysia, the first formal sit-down between the two sides since Duterte took office, as a "big milestone for peace in Mindanao".

MILF chief Murad Ebrahim said he welcomed fellow Muslim rebel Nur Misuari, chairman of the Moro National Liberation Front (MNLF), to join the transition commission to establish the "Bangsamoro" autonomous region in the south.

"For the inclusion of brother Nur Misuari, the MILF welcomes him joining because we believe there has to be inclusivity in finding a solution to the problem in the Bangsamoro homeland. We need all the players to be onboard," he said.

While there were some people in the southern Philippines inspired by the Islamic State jihadists, Ebrahim said "if the peace process was successful, they (IS) will not garner the people's support."

The Philippine Muslim separatists comprise three main groups -- the MNLF and breakaway factions the MILF and the Abu Sayyaf kidnap-for-ransom group.

Armed Muslim groups have been fighting since the 1970s for an independent Islamic state or autonomous rule in the south, which they regard as their ancestral home, and the conflict has claimed more than 100,000 lives.

The conflict has condemned millions of people across Mindanao to brutal poverty and created fertile conditions for Islamic extremism, with the Al-Qaeda-linked Abu Sayyaf and other hardline militants making remote areas their strongholds.