The commander, identified as Salip Idjal, and the other men were members of the Moro National Liberation Front, philippinedailyinquirer.net reported.
The surrender occurred about 8 a.m. in Zamboanga City, city officials said in a Twitter message.
Police spokesman Chief Inspector Ariel Huesca said 32 MNLF fighters had now surrendered and that government troops were conducting clearing operations.
The MNLF, formed in 1969, wants to create an independent nation in the southern Philippines.
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