Hundreds of gunmen attacked a lightly guarded military outpost at dawn, with some then taking over the school and using civilians as human shields throughout the day before fleeing at night, the military said.
"It's all resolved, all the hostages have been accounted for, no one was hurt," military spokesman Brigadier General Restituto Padilla told AFP by phone on Wednesday night.
The military said earlier that the gunmen had planted improvised bombs around the school, a small building in a rural area, and that soldiers had surrounded it.
Padilla and a local military spokesman said the militants were able to use the cover of darkness to escape, while leaving their 31 hostages unharmed. They said 12 children were among the hostages.
The unrest occurred in Pigkawayan, a farming town about 160 kilometres (100 miles) from Marawi city where fighters linked to the Islamic State (IS) group have been battling troops for a month in a conflict that has claimed hundreds of lives.
Armed forces spokesman Restituto Padilla said the attackers at Pikgawayan belonged to the Bangsamoro Islamic Freedom Fighters (BIFF), one of four groups in the southern Philippine region of Mindanao that have pledged allegiance to IS.
Local police said the BIFF attack may have been intended to help the militants in Marawi by distracting the military, although Padilla insisted it was unrelated.
Padilla said gunmen engaged in skirmishes throughout the day in and around Pigkawayan, while others occupied the school and using civilians seized from neighbouring homes as human shields.
Pigkawayan is part of a largely lawless areas with mixed Muslim-Christian communities where the BIFF, other Muslim rebels and political warlords hold sway. The town is surrounded by marshlands, mountains and farmlands.
About 200 gunmen were involved in the initial assault, according to Pigkawayan mayor Eliseo Garsesa.
Hardline groups
Muslim rebels have been fighting for more than four decades for an independent or autonomous region in the south of the mainly Catholic nation, with the conflict claiming more than 120,000 lives.
The major rebel organisations have signed, or are pursuing, peace deals with the government, but small hardline groups such as the BIFF have vowed to continue fighting.
Philippine President Rodrigo Duterte declared martial law across Mindanao, home to 20 million people, on May 23 immediately after fighters flying the IS flag rampaged through Marawi.
Their assault on Marawi ignited an unprecedented urban war that has claimed hundreds of lives and which Duterte has warned is part of an IS campaign to establish a base in Mindanao.
The fighting has left Marawi, the most important Muslim city in the Philippines, largely in ruins.
The militants involved in the Marawi fighting are mostly from the Maute and Abu Sayyaf organisations, which have united with the BIFF under the IS umbrella, according to the government.
The military has said foreign fighters, including those from Chechnya, Indonesia and Malaysia, have also joined the Marawi conflict.
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.
The BIFF was blamed for attacking Christian communities in Mindanao in 2008, triggering a conflict that claimed about 400 lives and forced 600,000 people to flee their homes.
Padilla said Wednesday's unrest at Pigkawayan was not related to the Marawi conflict, saying BIFF fighters were seeking to counter a military offensive against it.
"Apparently they wanted to get even after recent setbacks," Padilla told AFP.
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