The Philippine military said Tuesday it had killed 17 militants opposed to a peace deal between the government and the country's main Muslim rebel group even as a bomb wounded two civilians.

The improvised explosive went off in Datu Piang town, near the scene of the fighting in what the military suspects is an attempt to divert their forces.

More than 1,500 troops are involved in the offensive against the Bangsamoro Islamic Freedom Fighters (BIFF) in remote farming areas of the mainly Catholic country's Muslim south, regional military spokesman Colonel Dickson Hermoso said.

He said 17 BIFF members had been confirmed killed in this week's clashes, while two soldiers and one civilian were wounded in the fighting.

A pregnant woman and an eight-year-old girl were also wounded when the bomb went off near a marketplace shortly after noon, Hermoso said.

"It (the bomb) was planted where there are many innocent civilians. They want to relieve the pressure on their comrades that we have been pursuing," he told AFP.

The assault was launched on Monday, two days after the successful end of negotiations between the government and the Moro Islamic Liberation Front (MILF) aimed at ending a decades-long insurgency that has killed tens of thousands.

The BIFF is a small group of militants opposed to the peace effort, which has carried out many deadly attacks in recent years in a bid to derail the peace process.

National military spokesman Lieutenant Colonel Ramon Zagala said: "We consider them as peace spoilers, in that they may do actions that are detrimental to our peace process that is advancing greatly."

"Putting an end to the BIFF-armed challenge will be a big help to the autonomous Muslim political entity that will be created by the peace agreement," Hermoso said.

He said small skirmishes continued Tuesday in three farming villages on the edge of a marsh near the Datu Piang town, about 800 kilometres (500 miles) south of Manila.

Hermoso said the BIFF had about 120 "hardcore" members who were backed by scores of relatives and members of other armed groups opposed to the peace talks.

He said the soldiers were carrying out "law enforcement operations" to capture 25 of the militants, who had been charged with a string of criminal cases, including kidnapping, murder and extortion of civilians.

The MILF has been leading a rebellion since the 1970s aimed at winning independence or autonomy for the country's Muslim minority in the southern region of Mindanao, which they regard as their ancestral homeland.

But as the group sought a peace accord with the government, the BIFF broke away with its leader accusing the main Muslim rebel group of betraying Muslims' quest for independence.

After 18 years of negotiations, the MILF and the government agreed on Saturday to the final parts of a planned peace accord aimed at creating an autonomous Muslim region.

The accord is expected to be formally signed before the end of March.

Philippine President Benigno Aquino hopes to fully implement the peace plan before he steps down in the middle of 2016, but there are many legal, political and military obstacles that still need to be overcome.

One of those is the opposition of small splinter groups, such as the BIFF.

In 2008, it launched an attack on mainly Christian towns in the south, leading to the deaths of more than 400 people and displacing 750,000 others.