Philippine government and Muslim rebel negotiators met in Malaysia on Friday, forging ahead with talks on disarming the guerrillas despite a historic peace deal struck last year being thrown into doubt by a deadly clash.

The discussions marked the first formal sit-down between the two sides since a botched Philippine police anti-terror raid in the country's Muslim south last Sunday resulted in a firefight that killed 44 police commandos and shook the peace effort.

The Moro Islamic Liberation Front (MILF), which has waged a decades-long bloody insurgency, signed a protocol during an initial encounter Thursday in Kuala Lumpur that paves the way for disarmament.

Talks are expected to continue into the weekend at an undisclosed location as procedures are hammered out.

But the future of the entire peace effort has been called into doubt by the clash in Mindanao, with public calls growing in the Philippines for retribution against the rebels.

The police raid was aimed at capturing or killing a wanted Malaysian terrorism suspect but turned into a debacle when commandos were ambushed by fighters from MILF and the Bangsamoro Islamic Freedom Fighters (BIFF), a MILF splinter group.

MILF chief negotiator Mohagher Iqbal told AFP by phone that 11 MILF fighters also were killed, and 15 wounded, some seriously.

Last year's peace deal would create a southern autonomous region for the Philippines' Muslim minority with locally elected leaders by mid-2016.

Representatives of both sides at the Malaysia-hosted talks said they would not allow the bloodshed to derail the painstakingly achieved peace agreement signed last March.

"There is no other way to move forward," Iqbal said.

But President Benigno Aquino, who must convince Congress to approve the deal, is under mounting pressure to strike back at the rebels.

The Philippine police believe they managed to kill their target -- Zulkifli bin Hir, alias Marwan, a top suspect in the 2002 Bali bombings that killed 202 people, in the raid.

Iqbal insisted the MILF had no knowledge that Zulkifli was in their midst, and had no prior warning of the anti-terror operation.

He also said the MILF would not turn over to the government any guerrillas involved in the ambush, saying that was not required under ceasefire agreements.

The MILF and various other Muslim rebels have battled since the 1970s for independence or autonomy.

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 group and other hardline militants making remote areas their strongholds.

The Philippines is predominantly Catholic, but Islam was introduced to southern regions by Arab traders in the 13th century. (+++++)

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