President Benigno Aquino III said the military launched the assault to protect villages after Bangsamoro Islamic Freedom Movement fighters staged attacks in southern Maguindanao province. Troops were aiming "to seriously degrade their abilities to again act as spoilers," Aquino told reporters.
The rebels involved in the fighting have opposed peace talks between the government and the larger Moro Islamic Liberation Front, which were concluded over the weekend in Malaysia. They have promised to continue their uprising because the Malaysian-brokered talks would not lead to a separate homeland for minority Muslims in the south.
Regional military spokesman Col. Dickson Hermoso said 12 of the slain rebels have been identified with the help of village leaders, while others were found buried in graves in and near Ganta village in Maguindanao.
The fighting left one soldier dead and 12 others wounded by bombs hidden around a mosque and by rebel mortar fire, Hermoso said.
After two days of attacks, army troops captured a key rebel stronghold Wednesday that spanned two villages in a swampy mountain foothill in Maguindanao where the insurgents made bombs and carried out combat training. Several bombs and materials for making explosives were seized by troops, Hermoso said.
"It's like a bomb factory," Hermoso said. "We don't negotiate with groups like this who threaten innocent civilians. We run after them to enforce the law."
The offensive, which was supposed to end Wednesday, would be extended up to Saturday as troops pursue the retreating rebels, who have split into smaller groups, he said.
Rebel spokesman Abu Misry said a part of their stronghold had been taken by government forces but denied any of their fighters had been killed or captured. Only seven insurgents had been wounded so far in army shelling and helicopter rocket fire, he said.
"They can take our camps but if they don't capture us, they cannot stop our jihad," Misry said by telephone, referring to their term for holy war.
About 10,000 villagers have fled the fighting, which underscored the difficulty of ending violence in the country's south.
Aside from the main Moro rebel group that concluded negotiations Saturday with the government for a new Muslim autonomy deal in the south, at least four other smaller insurgent groups threaten the peace in the region.
Those groups include the Bangsamoro Islamic Freedom Movement and the smaller but more brutal Abu Sayyaf, which is notorious for bombings, kidnappings for ransom and beheadings.
Aquino said the new peace deal would bring the government and the 11,000-strong main Moro rebel group together to pursue outlaws who have long thrived in the conflict.