The suspect, identified as Mohammad Najib, is believed to have fled after troops overran one of their bomb-making camps on the southern island of Basilan on Thursday, said Colonel Joselito Rolando Bautista, the island's military commander.
Three militants and one soldier were killed when soldiers overran the camp of the Abu Sayyaf group, an armed band founded in the 1990s with seed money from Osama bin Laden's Al-Qaeda network.
"Mohammad Najib has been helping Ustadz Abbas Alam, the Abu Sayyaf leader in the area in making bombs and recruiting young people," he told reporters.
The two officials made the remarks while escorting reporters to the captured Abu Sayyaf outpost and showed off captured transceiver radio sets, nails, ammonium nitrate, rolls of wire, electrical components and iron pipes rigged with explosives.
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They also showed several black flags that are similar to the ones used by the Islamic State group in Iraq and Syria.
"The recovery is a big blow to the operation of the Abu Sayyaf and their plots to stage bombings were prevented," Bautista said.
Their attacks include the 2004 firebombing of a ferry off Manila Bay that killed more than 100 people.
Despite receiving training assistance from the United States, the Philippines has struggled to contain the Abu Sayyaf, whose leader last year pledged allegiance to the Islamic State movement.