Manila, Reuters—Philippine troops have killed about 17 members of a Muslim rebel faction, officials said, underscoring volatility in the resource-rich south as the government and the main rebel group enter the final, delicate stage of a peace process.

The government and the main Moro Islamic Liberation Front (MILF) reached a milestone in a 13-year peace process on the weekend, signing the fourth and final annex of a peace roadmap set out in 2012.

But the rebels, who have been fighting for autonomy in the Muslim-majority south for decades, have to give up their weapons in the final stage and that could lead to resistance and possibly violence from some of them, analysts say.

The latest violence flared in Maguindanao province on Monday when the military tried to serve arrest warrants against members of a splinter faction known as the Bangsamoro Islamic Freedom Fighters (BIFF) for kidnapping and killings.

Government forces were surrounding the rebels and skirmishing with them on Tuesday as they attempted to flee, an army spokesman said on Tuesday.

“We have enough troops to be able to handle the estimated 300 BIFF forces,” said Lt. Colonel Ramon Zagala, the army’s chief spokesman.

Troops had recovered the bodies of two rebels and officials said information from village officials and army personnel on the ground indicated 15 more rebels had been killed.

The fighting was unlikely to derail the peace process with MILF but it could slow it down, one analyst said, and it raised the prospect of more skirmishes over opposition to the decommissioning of rebel weapons.

“The pace of the process would be probably affected,” Julkipli Wadi, dean of the University of the Philippines’ Institute of Islamic Studies, said in a television interview.

“We can expect possible encounters, skirmishes and eventual refusal of other groups, they are not willing to lay down their arms, that could complicate things,” he said.

In September, members of another Muslim rebel faction who felt disadvantaged by the peace pact stormed into Zamboanga City, battling security forces for weeks after taking civilians hostage. About 200 people were killed.

The agreement on Saturday forged in Malaysia, which has been brokering talks since 2001, cleared the last hurdle to a pact to end more than 40 years of conflict that has killed 120,000 people, displaced about two million and stunted growth in a region rich in minerals and other natural resources.

The annexes of the peace pact will serve as the basis for legislation creating the Bangsamoro Basic Law that will formally set up a new regional government.