A Dutch birdwatcher held by Islamic State-linked militants was killed on Friday during a firefight between his kidnappers and soldiers in the southern Philippines, according to the military, which said he was shot by his captors as he tried to escape.

Ewold Horn had been held since 2012 by the Abu Sayyaf kidnap-for-ransom group and was fatally wounded as soldiers fought a 90-minute gun battle with the jihadists on their stronghold, Jolo island.

The Dutch foreign ministry confirmed Horn died in an "exchange of fire", adding that it was "investigating the exact circumstances" of his death.

Philippine Brigadier General Divino Rey Pabayo said in a statement that "Horn was shot by one of his guards when he tried to escape from the Abu Sayyaf during this morning's gunfight."

The military's account could not be independently confirmed.

The southern Philippines is home to numerous armed groups, several of which are linked to the decades-old insurgency aiming to create a Muslim homeland in the Christian majority nation's deep south.

Horn was on an expedition to photograph rare birds on the remote Tawi-Tawi island group in the southern Philippines when he was abducted by unknown gunmen and turned over to the Abu Sayyaf.

Horn was seized along with Lorenzo Vinciguerra, a Swiss national who managed to escape in 2014 during a gunbattle between soldiers and his captors.

Abu Sayyaf has been blamed for some of the worst terror attacks in Philippine history, including repeated kidnappings of foreigners who are usually ransomed off for huge amounts.

Philippine officials assert the group was behind the deadly January bombing of a Cathedral on Jolo island during Sunday mass that was the worst attack to hit the nation in years.

The bombing was claimed by the Islamic State, which has worked to maintain a presence in the Philippines as its caliphate crumbled in the Middle East.

Abu Sayyaf was active in the Philippines years before linking up with Islamic State, and has supported its violent activities with kidnapping.

The group has held hostages over the course of years as it negotiated ransoms, but has shown a willingness to kill its captives.

Abu Sayyaf beheaded German hostage Jurgen Kantner, 70, in 2017 after its demands for a roughly $600,000 ransom were not met.

Two Canadian hostages kidnapped from yachts moored at a marina on a tourist island in the southern Philippines were also beheaded in 2016 after demands for ransoms of similar amounts went unfulfilled.

The military said Friday that the group was believed to hold at least two Filipinos and a Vietnamese national, but it could not be sure they were still alive.

It added that a woman named Mingayan Sahiron, which the army identified as the second wife of a top Abu Sayyaf leader, was also killed in Friday's gunbattle.