By Agence France-Presse
The outrigger boat was attacked in the Moro Gulf off the Zamboanga peninsula on Mindanao island on Monday night, it said, citing an account by one of seven survivors.
A photograph released by the military showed the wooden fishing boat, recovered by the coast guard Tuesday, with a bloodied corpse atop another corpse.
"The other (crew) members jumped off the boat and survived," regional military spokesman Major Filemon Tan told AFP.
Tan said authorities suspect the fishermen were killed either as part of an extortion attempt or due to rivalry with the crew of other fishing boats.
The survivors swam to a small island, while the five unidentified gunmen left the area aboard their own boat, the spokesman added.
The waters off southwest Mindanao are troubled by piracy, including by Abu Sayyaf Islamic militants based on Basilan island and the Sulu island group near the port of Zamboanga.
The International Maritime Bureau said in a report Tuesday the number of maritime kidnappings worldwide hit a 10-year high last year.
It cited the Sulu Sea between eastern Malaysia and the Philippines as an increasing dangerous region.
The Abu Sayyaf boarded at least one cargo ship and several coal barges last year, abducting dozens of Indonesian, Malaysian and other foreign crew members. Some were later freed after the reported payment of ransoms.
Tan did not say if the Abu Sayyaf had any role in Monday's attack.
It came a week after suspected Abu Sayyaf gunmen on board two boats tried to board a Philippine-registered container ship off Basilan.
The ship's hull was hit by bullets but it continued on its course with all 27 crew members safe after the gunmen failed to board the vessel, Tan said.