An Indonesian hostage held by Muslim militants in the southern Philippines has swum to freedom but another drowned and a third man was shot in the back while escaping.

Key points: The men were being held by the Abu Sayyaf terrorist group on Simusa island in the southern Philippines

The men were being held by the Abu Sayyaf terrorist group on Simusa island in the southern Philippines The Malaysian man who was shot as he escaped is in a critical condition in hospital

The Malaysian man who was shot as he escaped is in a critical condition in hospital Abu Sayyaf is holding at least three more hostages, including a Dutch birdwatcher

Two Indonesians and a Malaysian separately escaped while Philippine marines were attempting to rescue them from the Islamic State-linked Abu Sayyaf group on Simusa island in southern Sulu province, regional military spokesman Lieutenant Colonel Gerry Besana said.

The dramatic escapes leave at least three more hostages 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.

The remaining captives include a Dutch birdwatcher, 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. They also 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 Malaysian, who was identified by the military as Jari Bin Abudullah, was shot by the militants when he ran away on Thursday as marines tried to rescue him and engaged his captors in a gun battle.

Philippine soldiers have been battling Islamic militants in the country's south for years. ( Reuters )

Government forces surrounded Simusa island, where a small community thrives near mangroves, to hunt down the remaining Abu Sayyaf gunmen.

Mr Bin Abudullah was airlifted to Zamboanga city, where he was in critical condition in a hospital, military officials said.

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

The three hostages were kidnapped off Malaysia's Sabah state on Borneo island in December 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.

AP