Troops bombarded the Abu Sayyaf camp on Jolo island before dawn with artillery and mortar fire. About 300 Philippine marine and army commandos battled around 200 militants, overrunning the camp by 7 a.m., said marine Brig. Gen. Juancho Sabban, commander of military forces on the island.
There were no immediate reports of casualties, or of militants being captured.
Sabban said he ordered a "surgical assault" on the camp after intelligence reports indicated an "unusual convergence" of leaders of the Abu Sayyaf group. These were believed to include one of their most wanted commanders, Radulan Sahiron, as well as Umar Patek, a member of the Indonesia-based Islamic extremist group Jemaah Islamiyah.
"I think they are planning to do something big, so we beat them to it (with) a pre-emptive strike," he told reporters in a telephone interview from Jolo, about 590 miles to the south.
"There was a bomb-making facility ... and it was destroyed through artillery fire," he said.
He said homemade bombs assembled at the camp, which are typically rigged from 81 mm mortar rounds, were similar to those used in attacks in nearby Zamboanga city and other areas.
The Abu Sayyaf, which is estimated to have 380 men, down from 1,000 in early 2000, is believed to have launched its last major attack in February 2005 with simultaneous bombings in Manila and two southern cities that killed eight people and wounded more than 100.
Despite problems, the guerrillas have continued to plot attacks, including against American soldiers who have been providing counterterrorism training to Filipino troops in the country's volatile south, police said.