They engaged in a two-hour firefight with prison guards, during which 154 inmates managed to go to the back of the prison and escape, according to prison warden Peter John Bonggat.
Xavier Solda, spokesman for the Bureau of Jail Management and Penology, said the jailbreak is the largest in the country's history.
Gunfire was heard for hours after the attack as army troops and police - some in armoured tanks - scoured through the surrounding forests for the 158 escaped inmates and the gunmen who freed them.
The region is a hotbed for Muslim rebels whose main objective is secessionism with some embracing terrorist attack techniques.
Manalundong, a member of the Moro Islamic Liberation Front (MILF), was said to have fought with policemen, but his family denied this and claimed he was shot dead by members of the Special Action Force.
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Shirlyn Macasarte, acting governor of North Cotabato, said her office had been tipped off about the plan by the Bangsamoro Islamic Freedom Fighters (BIFF) to free its members as early as the second quarter of previous year.
A follow-up report said five inmates were killed during a pursuit operation. "We have a manhunt operation".
Capalla said the attackers, clad in black suits and armed with high-powered firearms, rescued prisoners who are mostly members of the 105th Command of the BIFF under Ombra Kato.
At least four inmates had been recaptured after the jailbreak, Bongat added.
Carlos said they are ready to deploy additional policemen in some jail facilities once order is issued. They then scaled the walls with wooden ladders and stormed the compound, targeting cells that held high-profile inmates. "We belong to the one government, one administration and we will help other government agencies asking for the assistance of the PNP".