The five were part of a fishing fleet off the troubled southern island of Sulu when the gunmen attacked them on Friday, said Coast Guard spokesperson Lt. Jomark Angue.
Even as the five jumped overboard, the gunmen riddled them with bullets, then sped off. Only three of the bodies were recovered, Angue said.
The attackers were suspected to be pirates, Angue said, but it was unclear why they would attack the fishing boat crew.
Law enforcement sources said the attack might have been part of an extortion attempt by armed groups operating in Sulu.
Among the armed groups in Jolo are Muslim separatists who staged a bloody three-week siege in the southern city of Zamboanga in September.
The al-Qaida-linked Abu Sayyaf, a group known for the worst terror attacks in Philippine history, including bombings, kidnappings and banditry, are also active in Sulu along with other outlaw bands.