The authorities suspect the gunmen are linked to Islamist separatist groups.
Dozens of armed men stormed the jail and engaged in a shootout with guards, as prisoners fled in the chaos. One guard was killed and an inmate injured.
The Philippines, which is predominantly Catholic, has battled separatists in the south for decades, amid kidnappings, violence and jailbreaks.
The latest prison break took place at the North Cotabato District Jail near Kidapawan city, on the island of Mindanao.
Prison authorities said the gunmen showed up around 01:00 local time (17:00 GMT Tuesday), opening fire on the facility, which held more than 1,500 men.
The shootout lasted for about two hours, and in the confusion some prisoners fled to the back of the prison and climbed over the walls by stacking their beds, reported GMA News.
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