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Three hostages held by Islamic State group-aligned militants in the southern Philippines made a daring escape that left one drowned, another shot in the back in critical condition and another safe after swimming to his freedom, officials said on Saturday.

The two Indonesians and one Malaysian separately escaped while Philippine marines were attempting to rescue them on Simusa island in southern Sulu province over the last two days, regional military spokesman Lt. Col. Gerry Besana said.

The dramatic escapes leave at least three more hostages in the hands of the 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. The remaining captives include a Dutch bird watcher, Elwold Horn, who was kidnapped by the militants in 2012, and two Filipinos.

One of the Indonesians, Heri Ardiansyah, was plucked from the waters by marines on board a gunboat while they recovered the body of his companion, Hariadin, who drowned. The marines gunned down three Abu Sayyaf captors who were trying to chase the two Indonesians at sea, military officials said. 

The marines seized four assault rifles, a grenade launcher and various ammunition from the captors of the Indonesians, military officials said.

The Malaysian, who was identified by the military as Jari Bin Abudullah, was shot by the militants when he ran away Thursday as marines tried to rescue him and engaged his captors in a gunbattle. Government forces surrounded Simusa island, where a small community thrives near mangroves, to hunt down the remaining Abu Sayyaf gunmen.

"The act of shooting the kidnap victim is indicative of the Abu Sayyaf's hopelessness and desperateness as the militants are now surrounded by our pursuing troops," said Sulu's military commander, Brig. Gen. Divino Rey Pabayo Jr.

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

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 and poverty-wracked province where a few hundred Abu Sayyaf have survived in the jungles despite frequent military offensives.

Army troops on Friday clashed with about 80 Abu Sayyaf gunmen in Sulu's mountainous Patikul town in a fierce but brief gunbattle that left three soldiers and four militants dead and several wounded on both sides, the military said.

The Islamic State group issued a statement confirming it killed three and wounded 13 Philippine soldiers, but it said "the mujahideen returned safely to base".

The militants belong to an Abu Sayyaf faction led by commander Hajan Sawadjaan and aligned with the Islamic State group.

Sawadjaan is the main suspect in the bombing of a Roman Catholic cathedral during a Mass that killed 23 mostly churchgoers and two suspected suicide attackers on 27 January in Sulu's capital town of Jolo.