About 300 gunmen stormed the village of Malagakit in North Cotabato province at dawn Wednesday and engaged government forces in a firefight.
Mr Duterte has said politicians, including some linked to the illegal drug trade, may have covertly backed the militants, who stockpiled arms and supplies before launching their audacious plot in Marawi.
Almost 300 pro-Islamic State militants stormed a school in Philippines early on Wednesday and held students hostage, Reutersreported.
"They were taking advantage of the situation that we have a very lightly defended outpost and that they think our forces are elsewhere in the province", Padilla said.
Police first said 300 armed men from the Bangsamoro Islamic Freedom Fighters (BIFF) stormed the school on Wednesday.
"We can confirm that they occupied a school and there were civilians trapped".
Witnesses about a kilometre from the school said they could hear gunfire.
At least four rebels were killed and two government militiamen were wounded in the fighting, which caused almost 1,000 people in Malagakit and two nearby villages to flee to safety, the officials said.
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The latest attack took place as government forces continue to wind down operations against Maute fighters in Marawi City.
Local police said the BIFF attack may have been meant to help the militants in Marawi by distracting the military, although Padilla insisted it was unrelated.
Another military spokesman, captain Arvin Encinas, said the militants, who call themselves the Bangsamoro Islamic Freedom Fighters (BIFF), were holding some civilians hostage, but he was not sure how many. Community leaders in the area were called in to help in negotiations to rescue the hostages, Padilla said.
The BIFF, which broke away from the Moro Islamic Liberation Front nearly a decade go, is one of the armed groups in Mindanao that government claims have pledged allegiance to the Islamic State.
He said they would be freed in due time.
Clashes between Islamists and the Philippine military forced prompted President Rodrigo Duterte to declare martial law in the entire island in May.
IS has ambitions of setting up a caliphate in Southeast Asia - home to largely Muslim nations like Indonesia and Malaysia - as the group loses territory in Iraq and Syria.
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