Intelligence reports showed the assaults killed at least four militants, possibly including a Malaysian, and reportedly wounded the main target, Isnilon Hapilon, Defense Secretary Delfin Lorenzana told The Associated Press.
He said Hapilon apparently managed to flee from a camp in the mountainous hinterlands of Butig town in southern Lanao del Sur province.
"Army troops are still in hot pursuit," Lorenzana said.
Airstrikes targeted Hapilon's group on Wednesday and Thursday. Hundreds of troops, backed by artillery fire, then began pursuing him and other militants from the so-called Maute group in Butig, military chief of staff Gen. Eduardo Ano said.
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Lanao is about 830 kilometers (520 miles) south of Manila. President Rodrigo Duterte has repeatedly warned that the emergence of Islamic State-influenced militant groups is fast looming as a major national security threat. While pursuing peace talks with two large Muslim rebel groups in the predominantly Roman Catholic nation, he has ordered the military to destroy smaller but brutal extremist groups like the Abu Sayyaf, which is dreaded for cross-border kidnappings, beheadings and bombings.
"I am pleading. Do not allow the Maute and the other terrorist groups to enter and seek refuge in your camps," Duterte said in a speech after meeting Ano, Lorenzana and military commanders in the south. "If you share a part of your territory, you don't allow us to enter, and you give them protection ... Forget about peace, let's just fight."
A wave of Abu Sayyaf kidnappings of crewmen on ships, mostly from Indonesia and Malaysia, has sparked a regional security alarm.