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.