Attempts by Philippine authorities to arrest several current and former commanders of the 11,000-strong Moro Islamic Liberation Front and allied gunmen accused of kidnappings for ransom and other crimes sparked separate deadly clashes last week in Zamboanga Sibugay province and on Basilan island.
The Moro group has been waging a bloody fight for self-rule in southern Mindanao region, homeland of minority Muslims in the predominantly Roman Catholic Philippines. A cease-fire has held since 2008.
President Benigno Aquino III said Monday his administration would continue talks with the insurgents but seek the arrest of criminals, including those from the rebel group.
The 120,000-strong military suffered one of its biggest losses in years in Basilan last week when troops tried to capture a fugitive rebel commander and other outlaws, igniting daylong fighting that killed 19 soldiers.
Fearing more clashes, nearly 6,000 villagers have fled from Al-Barka and outlying towns in Basilan, a predominantly Muslim province about 550 miles (880 kilometers) south of Manila, Office of Civil Defense Administrator Benito Ramos said.
In Zamboanga Sibugay, also in the south, about 10,800 villagers have fled to safety from three towns, including in coastal Payao, where air force OV-10 bomber planes, naval gunboats and about 700 army troops and police have been trying to flush out more than 120 former Muslim rebels and bandits encamped in a hilly forest, officials said.
Zamboanga Sibugay police chief Ruben Carriaga said military aircraft staged bombing runs for a second day Tuesday in Payao. Troops assaulted the bandits after OV-10 planes dropped bombs on their lair Monday but were met by heavy machine-gun fire that killed two soldiers, he said.
"Our men couldn't penetrate the area yet because of heavy volumes of fire," Carriaga said, but added the gunmen, who include members of the Moro Islamic Liberation Front, have been surrounded.
The gunmen, accused of kidnappings for ransom, extortion and other crimes, may be holding at least one kidnap victim, officials said.
Rebel spokesman Von Al Haq has urged the military to stop the Payao offensive, saying it has displaced many civilian supporters of his Moro insurgent group and was endangering a cease-fire.