The takeover is tied to a centuries-old conflict with Muslims loyal to a sultan once powerful in the southern Philippines and parts of Malaysia. CNN said 12 of the militants were killed along with two Malaysian police officers in a gun fight Friday.
The New York Times said the militants arrived on the island of Borneo Feb. 12 to re-establish long dormant claims to ownership of the area and resisted several peaceful pleas to relinquish power prior to Friday's gunfight.
"Because of the path you have taken, what we have been trying to avoid has come to pass," Aquino said. "If you have grievances, the path you chose was wrong. The just and, indeed, the only correct thing for you to do is to surrender."