Eight Dawlah Islamiyah militants were suspected of carrying out the attack on Mindanao island, army brigade commander Brigadier General Yegor Rey Barroquillo said.
Five have been killed in manhunt operations, one has been detained, and another two were still on the run, he said.
Among the dead was Khadafi Mimbesa, who went by the alias of “engineer”. The Armed Forces of the Philippines said he was the “mastermind” behind the bombing.
Mimbesa was wounded in a shoot-out between army soldiers and militants hiding out at a mountain farm near the remote southern municipality of Piagapo late last month, Barroquillo said.
Nine militants, including three suspects in the bombing, were killed in the fighting.
Mimbesa was wounded but escaped and died days later while being cared for by a supporter, Barroquillo said, citing intelligence reports.
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Survivors of Philippines Catholic church bombing recall deadly blast
Survivors of Philippines Catholic church bombing recall deadly blast
In the statement, military chief General Romeo Brawner urged other members of the militant group to surrender and “avoid the same fate as your dead comrades”.
Militant attacks on buses, Catholic churches and public markets have been a feature of decades-long unrest in the south.
Manila signed a peace pact with the nation’s largest rebel group, the Moro Islamic Liberation Front, in 2014, ending their deadly armed rebellion.
But smaller bands of Muslim fighters opposed to the peace deal remain, including militants professing allegiance to Islamic State group.