Judnam Jamalul, one of those killed, and known by his alias, Black Killer, is among 17 Abu Sayyaf leaders and members, who are wanted by the United States for their role in attacks on American citizens.
Khadaffy Janjalani, the group's chief, is among them.
In another operation, two other Abu Sayyaf members, who allegedly took part in an assault on a government hospital in 2001, were arrested in southern Zamboanga city, said Lieutenant-Colonel Bartolome Bacarro.
The Abu Sayyaf abducted three American tourists and 17 Filipinos from a resort in May 2001.
One of the Americans was beheaded soon after the kidnapping and another was killed during a military rescue operation the following year.
Bacarro said the troops recovered the boat used by the group, an M-16 rifle and an M203 grenade-launcher following the clash in the waters off the Philippines' southernmost province, about 1,050km southwest of Manila.
No other details were immediately available, he said.
Major Eugene Batara, spokesman for the military's Southwestern Command, said two other Abu Sayyaf members were arrested in a restaurant in Zamboanga.
He said the two were allegedly involved in the siege of a government hospital in the nearby island province of Basilan where the gunmen took a nurse hostage. The nurse later died in rebel hands.