After forcing open the cells, they herded out three inmates being tried for their alleged involvement in a 2003 bomb attack in the volatile Mindanao region of the south.
Dozens of other Muslim inmates out of the 789 prisoners also escaped, he said.
Emmanuel Pinol, the governor of North Cotabato, said: "We were caught with our pants down."
He said the attackers may have been Muslim separatists belonging to the Moro Islamic Liberation Front (MILF) in his province, adding that he had "ordered police to shoot these very dangerous people if they will resist arrest".
"They are better dead than a menace to our communities." Eid Kabalu, an MILF spokesman, denied his group attacked the jail.