Rebel forces led by Nur Misuari, the Moro National Liberation Front, or MNLF, attacked Zamboanga City Sept. 9. Since then, more than 100 people have been killed and more than 100,000 of the city's 1 million people have fled, China's state-run Xinhua news agency said.
Aquino said there are about 300 MNLF fighters left in the city and he urged them to lay down their arms or face the full weight of the Filipino army.
Misuari, 71, is not thought to be among the troops fighting in the city.
Aquino said his government would "fight violence with violence."
"For the remaining forces of the enemy (let me say that) life is sacred to me. You might want to assess if your life is still valuable, and it's not yet too late to bring an end to this," Aquino said.
Misuari has a long history of violent clashes with the official government in the Philippines. He signed a peace accord in 1996 that gave him a measure of autonomy over Jolo, the southern-most tip of the Philippines archipelago, but abandoned the deal after the government made a separate deal with another rebel leader, leading to the attack in Zamboanga, Xinhua said.