The Southeast Asian nation has for decades been plagued by insurgencies by rebels in its southern islands, with President Rodrigo Duterte seeking to promote broad peace in the predominantly Catholic country.
Prison warden Peter Bongat told media that the gunmen opened fire at guards at the North Cotabato District Jail in Kidapawan city around 1:00 AM (5:00 PM GMT).
The prison warden said, 158 managed to escape of the jail's 1,511 prisoners , and four were recaptured. He said, "It's well-planned. Escapees used blanket as their getaway...We have a manhunt operation,"
The rebel commander belonged to the Moro Islamic Liberation Front (MILF) based on initial information, Bongat said.
In 2014, the government signed a peace deal with the MILF, the biggest Muslim rebel group, but clashes still occur with smaller groups.