Philippine security forces and a Muslim rebel group clashed Sunday in the country's south killing at least six police officers, both sides confirmed, in violence rarely seen since the signing of a peace treaty.

Police commandos and Moro Islamic Liberation Front (MILF) members fought near the remote town of Mamasapano on the main southern island of Mindanao before dawn, regional military spokesman Captain Joan Petinglay said.

"Ceasefire monitors are now on the ground to separate the forces and remove the casualties," said Petinglay, speaking to AFP by telephone from the neighbouring town of Shariff Aguak.

Regional police chief Noel Armillo told AFP that they have so far recovered the bodies of six police officers, adding that the extraction of more is ongoing.

No rebel bodies had been recovered, he said, and he declined to say how many officers remain unacounted for.

"Operational information from the field (is) still sketchy at the moment but what we know so far is that there is an ongoing operation in the area against a high-value target believed to be behind the recent spate of bombings in Central Mindanao," national police chief Leonardo Espina said in a statement.

Mohagher Iqbal, the lead MILF negotiator in a landmark peace deal signed in March last year, also confirmed the incident, but would not say how many fighters were wounded or killed.

- Decade-long rebellion -

The 10,000-member MILF had agreed to end decades of rebellion in the mainly Catholic nation in exchange for a proposed law now being debated in parliament that would give the minority Muslims self-rule in several southern provinces.

"This is the first encounter between the MILF and (government forces) this year. Hopefully, this will be the last," Iqbal told AFP by telephone.

He said the police had entered an MILF-influenced area without notifying the group first, while searching for members of the Bangsamoro Islamic Freedom Fighters (BIFF), which disagrees with the peace talks and broke away from the MILF in 2008.

"They (police) ran into an MILF force. The ceasefire monitors are now in the area," Iqbal added.

"We heard some people were killed, but I believe this will not affect the peace process," he added.

Both Iqbal and Petinglay said a joint government-MILF ceasefire committee and a small international monitoring team of soldiers and police from Malaysia and other countries had arrived in the area by the afternoon to "disengage" the two groups.

The clash in Mamasapano, about 900 kilometres (559 miles) south of Manila, was only the second since two soldiers and 18 Muslim gunmen were killed in a clash on the southern island of Basilan in April 2014.

Such incidents once broke out with much greater frequency prior to the signing of the treaty, during a rebellion that has claimed tens of thousands of lives.

After the April fighting, the government accused the MILF of helping Islamic extremists under attack from security forces. The group acknowledged four of its members were killed.

Since the peace deal was struck, government forces have been going after the BIFF, a group of several hundred Muslim gunmen who last year pledged allegiance to Islamic State fighters in Iraq and Syria.