A Filipino soldier kidnapped last week in the southern Philippines by Abu Sayyaf fighters was found beheaded hours after government troops killed three more members of the ISIL-linked group in a clash elsewhere.

The head of Sergeant Anni Siraji of the Army's 32nd Infantry Battalion was found 50 metres away from his body in Patikul town in Sulu, Brigadier General Cirilito Sobejana, commander of the Joint Task Force Sulu, said.

Sobejana said Siraji was probably abducted and executed because of his involvement in peace initiatives in Sulu.

"He is involved in peace efforts. He is not actually a combatant. We are using him to engage stakeholders because he is a Tausug [like most Abu Sayyaf]," he said.

Earlier on Sunday, the military said troops had killed three more Abu Sayyaf fighters on the resort island of Bohol where they were hiding after a failed attempt to kidnap tourists.

The military was pursuing two or three more insurgents still at large in Bohol, a long way to the north of their strongholds in the far south of the predominately Christian country.

"We have reports indicating that they were also wounded and running out of supplies," said Colonel Edgard Arevalo, chief of the military's public affairs office.

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A group of about 10 fighters infiltrated Bohol this month. Western countries have issued travel warnings about visiting the island.

Six were killed in a clash on April 11 and one last week.

Among those killed was their leader, who had been involved in the kidnap and execution of Canadian and German nationals in recent months, the Philippine military has said.

The military has been struggling to wipe out Abu Sayyaf, which originally had Muslim separatist aims but now engages mostly in banditry and piracy.

The group has been holding more than two dozen captives, most of them Vietnamese sailors, who are easy prey for the fighters equipped with small, fast boats.