President Benigno Aquino III's comments came Friday during a speech at the armed forces of the Philippines' headquarters in the southern town of Zamboanga, CNN reported.
Since Monday, Muslim rebels have been in a standoff with security forces in Zamboanga. The rebels have taken roughly 170 people hostage, some of whom have managed to escape.
"There are limits, if there is an increased threat to the safety to innocent civilians," Aquino said. "There are lines that they cannot cross. If they cross those lines, we will be obligated to use the state's force against them."
Zamboanga Mayor Isabelle Climaco Salazar said Friday negotiations to bring the situation to a peaceful end have failed and city officials will defer to Aquino for a plan of action.