Two soldiers were wounded in the assault on the camp of about 50 Dawlah Islamiya group fighters near the town of Maguing in Lanao del Sur province.
Air force fighter jets dropped a dozen bombs as army troops launched a ground attack, regional military commander Lieutenant General Alfredo Rosario Jr said.
The gunmen fled after the air strikes and were being pursued, Rosario and other military officials said.
The assault was staged far from rural communities to prevent civilians from being caught in the crossfire, they said.
Military officials said troops were continuing to clash sporadically with fleeing militants led by a militant commander they identified as Abu Zacharia.
Members of Dawlah Islamiya were involved in a 2017 siege of southern Marawi city, where hundreds of militants waving Islamic State group-style black flags occupied commercial buildings and villages and took hostages.
Filipino troops, backed by US and Australian surveillance aircraft, quelled the five-month siege, which left about 1200 people dead, mostly militants.
The military has been launching offensives against small armed groups allied with the militants who laid siege on Marawi, including the Abu Sayyaf, which has been blacklisted by the US and the Philippines for past bombings, ransom kidnappings and beheadings.
