The clashes have erupted amid ongoing talks between the government and the rebels, who have waged a decades-long campaign for self-rule.
Philippine aircraft and artillery bombed rebel positions for a second day on Monday, Reuters reported.
Violence flared last week after the country’s Supreme Court decided to suspend plans for an extended Muslim homeland in the south, prompting some Moro Islamic Liberation Front rebels to take control of mainly Christian villages in North Cotabato province, a poor farming region in Mindanao, Agence France-Presse reported.
Some rebels left on orders from MILF leadership, but others defiantly set up defensive positions.
The 12,000-strong MILF has waged a 30-year guerrilla campaign for a separate Islamic state in the south of the largely Christian Philippines.
The National Disaster Coordinating Council said 129,819 people have been displaced from 42 villages in North Cotabato. The refugees are being housed in 43 government evacuation centers in the province in the southern island of Mindanao, said Glenn Raboza, an NDCC executive officer, according to AFP. The government was providing water, sanitation and food.
In the battle for 15 villages in North Cotabato province, seven rebels, three soldiers and three civilians were killed, the military said, according to Reuters. The MILF said four of its members had been killed and three wounded.
Manila, which is smarting from accusations it had abandoned majority Catholics, has vowed to flush hundreds of MILF rebels out of the area. The military said two villages were now clear of rebels.
“We are conducting air strikes, close air support to our ground forces. Our forces are inching in towards the different barangays (villages) with the objective of clearing them,” said Lt. Gen. Cardozo Luna, deputy military chief. “Of course we use big weapons like artillery.”
The military insisted the clashes would not spread, but MILF members attacked a town on the island of Basilan, about 125 miles southwest of where the main fighting was taking place, and disrupted voting in local elections there.
The separatist MILF had called for elections in the six-province Autonomous Region in Muslim Mindanao to be cancelled because they want a new Muslim homeland with more political powers established as part of a peace deal.
The two sides had reached agreement covering the territorial makeup of a future expanded Muslim region, but the signing of the accord was halted last week by the Supreme Court, acting on a petition filed by Christian politicians in North Cotabato who are wary of losing land and power to the Muslims.
There were concerns that the deadly clashes could spread beyond North Cotabato, a predominantly Christian province of more than a million people located near the Philippines’ sprawling Muslim autonomous region.
About 1.5 million Filipino Muslims in the region voted under heavy security Monday for a new governor, vice governor and other posts in the regional assembly. The five-province region has a history of insurgent and factional violence, but the nearby fighting did not immediately affect the election.
The government had given the estimated 800-1,000 MILF guerrillas until Friday morning to vacate 15 villages in five North Cotabato townships.