The army said it had launched an investigation into Monday's incident, which came shortly after the government put on hold on-and-off peace negotiations aimed at ending one of Asia's longest-running insurgencies.

"It was a vegetated, jungle area and you could not see through the (men's) positions," Captain Francis Agno, spokesman for the army division involved in the 30-minute firefight, told AFP.

"After the encounter, the troops found out that it was the police they clashed with. There is now a thorough investigation to shed light on the incident," he said, adding it was a joint probe with the police.

Police said their colleagues were also on patrol in the area near the town of Santa Rita, about 550 kilometres (340 miles) southeast of Manila.

They said six policemen were killed and nine wounded, while the army unit did not report any casualties.

The clash occurred on the impoverished eastern island of Samar, one of the last redoubts of a 49-year-old rebellion by communist New People's Army guerrillas which has claimed 30,000 lives according to the government's count.

Peace talks have been conducted on and off for 30 years and President Rodrigo Duterte decided to hold off for three months the resumption of negotiations originally scheduled this month.

Monday's clash was not the first fatal friendly fire incident involving Philippine security forces.

Last year two military air strikes accidentally killed at least 12 soldiers as troops fought to retake the southern city of Marawi from pro-Islamic State group militants.