The Philippines said Wednesday it was confident a peace deal with the country's largest Muslim rebel group would hold despite fresh clashes that left four of its members dead.

The fighting took place just two weeks after the 10,000-member Moro Islamic Liberation Front (MILF) signed a peace deal to end their decades-old rebellion that had claimed tens of thousands of lives.

MILF fighters helped a group of Islamic extremists fighting government forces on Friday, but did so without their top leadership's permission, President Benigno Aquino's top peace adviser Teresita Deles said.

Two soldiers and 18 gunmen were slain in the clashes on the remote southern island of Basilan, the military said, while the MILF acknowledged four of its members were among those killed.

"This will not affect the entire peace process," Deles told AFP.

"The resolve of both parties has not waned."

The peace treaty aims to set up an autonomous Muslim area in the south of the mainly Catholic nation early next year. The MILF is expected to disarm and put up candidates for a regional parliament in May 2016.

"We are still confident that the MILF leadership can bring a huge bulk of their fighters into the fold of the law," Deles said, though conceding a "small number" of the rebel force may opt to ignore the peace deal.

This faction would be "subjected to law enforcement activities", she added.

MILF vice chairman Ghazali Jaafar had denounced the killings, and asked an independent body monitoring a ceasefire between the rebels and the government to investigate the fighting which he alleged was initiated by the military.

The military has said the slain MILF fighters were apparently drawn into the fighting because they had relatives among the Abu Sayyaf group involved in the shootout.

The Abu Sayyaf is a small gang of self-styled Islamic militants blamed for the country's worst attacks, including bombings, beheadings and kidnappings.

Military officials said it was founded with seed money from the Al Qaeda group in the 1990s, although it has since degenerated into a purely criminal gang.

Abu Sayyaf gunmen are believed to be still holding a number of foreign hostages on another island in the restive southern region, possibly including a Chinese tourist seized from a Malaysian dive resort on April 2.