The Philippines' chief peace negotiator with Muslim rebels called Thursday on breakaway guerrillas still fighting the government to turn themselves in, as the death toll from this week's clashes rose to 41.

Negotiator Miriam Coronel said the main Muslim rebel group, the Moro Islamic Liberation Front (MILF), was working with government forces to contain the breakaway group and stop the fighting spreading from remote villages in the southern island of Mindanao.

Clashes broke out this week between troops and members of the Bangsamoro Islamic Freedom Fighters (BIFF), a small breakaway faction of the MILF which opposes the peace talks.

Regional military spokesman Colonel Dickson Hermoso said 40 BIFF members and one soldier had been killed while 13 soldiers had been wounded.

About 10,000 civilians had fled their homes due to the violence, he told AFP.

The new clashes broke out just two days after the government and the MILF successfully concluded years of negotiations aimed at ending a decades-long insurgency that has killed tens of thousands.

The BIFF has carried out several deadly attacks in recent years to try to derail the peace process.

"The ongoing military operations are geared at degrading the BIFF's capability to continue to cause harm to the government forces, civilians and the peace process," Coronel said in a statement.

"We call on the members and the leaders of the BIFF to put down their arms and be part of the process. We ask them to listen to the plea of their own brothers and sisters to give peace a chance."

Visiting British Foreign Secretary William Hague said the success of the negotiations with the MILF "is a testament to the vision and determination of (Philippine) President (Benigno) Aquino and all those involved".

"We know from our own experience in Northern Ireland that implementation brings its own challenges, but it will also bring rewards, both for Mindanao and for the whole of the Philippines," he said.