Soldiers, backed by artillery, attacked guerrillas of the Bangsamoro Islamic Freedom Fighters (BIFF) in a remote village on the southern island of Mindanao, triggering fighting that sent hundreds of civilians fleeing, the military said.
Regional military spokesman Dickson Hermoso told AFP the attacks were launched in a bid to arrest about 25 leaders of the BIFF, a small group of between 250 and 400 militants that is opposed to the peace process.
The attacks began on Monday morning and were continuing throughout the day, according to Colonel Hermoso, who said there were no immediate casualties.
Hermoso said the Moro Islamic Liberation Front (MILF), the 12,000-strong rebel organisation that wrapped up peace talks with the government on the weekend, was helping the military.
"The MILF are part of the law enforcement operations. They are just securing their communities so those (BIFF fighters) cannot enter. They are also angry at the BIFF," he told AFP.
MILF military spokesman Von al-Haq confirmed that the military had coordinated with the MILF before the attack.
"The BIFF cannot enter (our territories.) We have a line where we have re-positioned (personnel). If they run there, they cannot enter there unless they are surrendering," he told AFP.
The MILF has been leading a rebellion in the southern Philippines since the 1970s aimed at winning independence or autonomy for the country's Muslim minority in Mindanao, which they regard as their ancestral homeland.
About 150,000 people are estimated to have been killed in the conflict.
After 18 years of negotiations, the MILF agreed Saturday on the final parts of a peace accord that would give Muslims a large degree of autonomy in the south, including control of much of the region's natural resources.
The peace accord is expected to be signed within weeks and President Benigno Aquino is aiming for it to be fully implemented before he steps down in mid-2016.
However it must still clear other hurdles, including congressional approval and a regional plebiscite, as well as the opposition of smaller rebel groups such as the BIFF.
The BIFF broke away from the MILF gradually after its leader, Saudi-trained cleric Ameril Umbrakato, accused the main Muslim group of betraying the region's quest for independence.
Umbrakato led attacks against mostly Christian towns in the south in 2008, leading to the deaths of more than 400 people and displacing 750,000 others.