A platoon of soldiers was operating in a remote village on Samar island when they mistook a group of police officers as communist New People's Army (NPA) guerrillas, and opened fire, said Major-General Raul Farnacio.
Farnacio said it was an "unfortunate incident".
"When you are in a highly vegetated area, it's hard to distinguish who you are up against," he said, adding there were no casualties among the soldiers.
"The other side also returned fire. We are still conducting an investigation to determine how these two groups came close to each other."
National police chief Oscar Albayalde said police teams would go to the area to investigate.
The NPA has been fighting the government for nearly 50 years.
More than 40,000 have been killed in the insurgency and economic growth in resource-rich areas has been stunted.