An Indonesian hostage held by Muslim militants in the southern Philippines has swum to freedom in an escape that unfolded like the climax of a Hollywood action movie.

One of his companions drowned in the daring bid, while a Malaysian captive was wounded in the back as Islamist Abu Sayyaf guerillas opened fire.

Officials said the trio made their individual escapes amid the chaos that erupted while Philippine marines were attempting to rescue them from Simusa island in southern Sulu province, regional military spokesman Lt Col Gerry Besana said.

At least three more hostages remain in the custody of Abu Sayyaf, which is blacklisted by the United States and the Philippines as a terrorist organisation due to its brutal history of bombings, ransom kidnappings, extortion and beheadings.

Three other captives are still being held, officials said, naming a Dutch bird watcher, Elwold Horn, who has been held for almost seven years, plus two unnamed Filipinos.

One of the Indonesians, Heri Ardiansyah, was plucked from the waters by marines on a gunboat while they recovered the body of his companion, known as Hariadin, who drowned.

The marines shot dead three of the Abu Sayyaf militants as they chased the two Indonesians through waters off the small and isolated island, military officials said.

The Malaysian, identified by the military as Jari Bin Abudullah, was shot by the militants as marines engaged his captors in a gun battle.

Government forces have surrounded the island to hunt down the remaining Abu Sayyaf gunmen.

The wounded Malaysian was airlifted to Zamboanga city, where he was hospitalised in critical condition, military officials said.

The Islamic State group issued a statement claiming it killed three marines and wounded 13 others, insisting “the mujahideen returned safely to base.”

The three hostages were kidnapped off Malaysia’s Sabah state on Borneo island in December last year and taken by speedboat to Sulu, the predominantly Muslim province where several hundred Abu Sayyaf guerillas continue to defy repeated government offensives.

–with AAP