Philippine troops rescued two abducted Indonesian sailors in a Sunday pre-dawn raid on an militant stronghold which left two dead, a military official said.

A soldier and a militant of kidnap-for-ransom group Abu Sayyaf -- which was behind some of the nation's worst attacks -- were killed during a 30-minute gunfight in the mountainous town of Panamao on the southern island of Jolo.

‘During the firefights, the two victims managed to scamper away (from the militants) and we were able to rescue them,’ military commander Lieutenant General Cirilito Sobejana told AFP.

The pair were among three Indonesian sailors abducted by the militants in September off Malaysian waters near the southern tip of the Philippine island of Mindanao.

Sobejana said a military operation was underway to rescue the other Indonesian captive.

‘He could have escaped or militants could still have him, so we are expecting another firefight,’ Sobejana said.

The rescue came a month after a British man and his wife were freed by soldiers and said they were threatened with beheading by militants if they did not deliver a ransom.

In May, Dutch birdwatcher Ewold Horn was killed by his captors as he tried to escape during a rescue operation, the military said, after being held captive for seven years.

The Abu Sayyaf group is also blamed by authorities for an Islamic State-claimed suicide bombing of Sunday mass at a Catholic cathedral in Jolo in January that killed 21 people.