The Philippine military has launched a major offensive against a splinter rebel group, two days after negotiations with the country's main Muslim rebel group to end a decades-long insurgency that has killed tens of thousands successfully ended.

Soldiers, backed by artillery, attacked guerrillas of the Bangsamoro Islamic Freedom Fighters (BIFF) in a remote village on the southern island of Mindanao on Monday, triggering fighting that sent hundreds of civilians fleeing, the military said.

Al Jazeera's Jamela Alindogan, reporting from the capital, Manila, said that the fighting apparently erupted after the military tried to serve warrants of arrest against the BIFF, which is fighting for an independent Islamic state.

In 2008, the BIFF broke away from the main rebel group Moro Islamic Liberation Front (MILF) that is now on the brink of signing a final peace deal with the Philippine government.

Since breaking away from the MILF, the BIFF has been accused of carrying out armed robberies and bombings in several cities in Mindanao.

On Sunday, the government and MILF negotiators sealed the final phase of talks in Malaysia that would pave the way for the laying down of arms by rebels in exchange for greater autonomy.

The BIFF, however, said that the deal is not inclusive and does not represent the needs of their people.

Under the peace deal, an existing five-province Muslim autonomous region is to be replaced by a more powerful, better-funded and potentially larger region to be called Bangsamoro.

Despite the milestone, both the government and the rebels acknowledged that violence would not end overnight in a region that has long grappled with a volatile mix of crushing poverty, huge numbers of illegal firearms, clan wars and weak law enforcement.