The Philippines' largest Muslim militant group has launched a deadly offensive against a splinter faction that has pledged allegiance to the Islamic State group, police said Saturday.

The fighting between the two groups began about two weeks ago in the marshy farmlands around the southern town of Datu Salibo on Mindanao island, regional police spokeswoman Tara Leah Cuyco said.

Clashes between the Moro Islamic Liberation Front (MILF) and its offshoot, the Bangsamoro Islamic Freedom Fighters (BIFF), took place on Friday and Saturday, with six fighters from the original group killed.

"The MILF is trying to force the BIFF out of the area. They do not want any trouble," Chief Inspector Cuyco told AFP.

A MILF guerrilla leader told a video journalist working for AFP on Saturday: "We do not want them here. It's an order from the higher-ups."

The MILF, which has more than 10,000 fighters, has waged a decades-long guerrilla war, first for independence and later autonomy for the large Islamic minority in the south of the largely Catholic Asian nation.

It signed a peace treaty with the government in 2014 and is observing a ceasefire with the government while waiting for the passage of a proposed law that would grant self-rule to the Muslim areas of the Mindanao region.

Senior MILF leaders have warned President Rodrigo Duterte to deliver on government commitments under the peace accord, chiefly the autonomy law, or risk frustrating MILF members and causing them to defect to the BIFF and other pro-IS groups.

The BIFF, said by the military to have a few hundred armed fighters, has been among several small armed groups in Mindanao that have pledged alliance to the IS.

The fighting comes as the military fought a near three-month battle in Marawi, a Muslim city 100 kilometers to the north.

The fighting in Marawi is being led by two other Muslim rebel factions, the Maute group and the Abu Sayyaf.

The Marawi battle has left 573 militants and 128 soldiers and police dead, along with at least 45 civilians, according to an official tally.