President Rodrigo Duterte pledged an impartial government investigation of Monday's violence in southern Jolo town and promised in a late-night address to military commanders that anyone found guilty will be punished.

"Do you want to kill five to six policemen there in the station? What good will it do?," said the blunt-speaking Duterte, who wore a face mask to protect against the coronavirus.

Duterte asked commanders to ensure their forces remain calm and added that police, like government troops, perform a vital role in maintaining law and order.

He cited a Muslim rebel leader, Nur Misuari, whom he appointed as a special envoy to the Organisation of Islamic Conference despite his involvement in past rebel attacks that killed many soldiers.

"Why is he there?" Duterte asked. "That's the reality of it all. You have enemies that you cannot kill because you can still use them... We need the police out there."

An initial police report said the four soldiers were killed in a "misencounter" with a group of police officers.

The army has said its two officers and two enlisted men were on a mission against Abu Sayyaf militants when they were flagged down and later fatally shot by police even after the soldiers identified themselves.

Army chief Lieutenant General Gilbert Gapay angrily condemned the police report as a fabrication, citing security videos and witnesses accounts which he said showed that there was no exchange of fire.

The police later changed the term "misencounter" to a "shooting incident".

"It was murder... It was a rubout," Gapay said on Tuesday at a Manila airbase where the bodies of three of the soldiers were flown.

Australian Associated Press