The incident happened on Monday off Basilan province, a stronghold of Muslim rebels.
Three men were also wounded in the incident.
Police have identified several suspects involved but no-one has been arrested yet.
“They (the victims) were fishing on another group’s turf,” regional military spokesman Lt Col Randolph Cabangbang told the Agence France Presse news agency.
He added that the possibility of Islamist militants being involved in the incident had so far been ruled out.
The fishermen were aboard three wooden vessels off Sibago island in Basilan when the gunmen in speedboats opened fire.
The shooting was discovered by other fishermen in the area. The victims were residents of Pagadian city, 160km (100 miles) north-east of Basilan.
A survivor reportedly told police that they had been warned to stay away from the area where the attack took place.
Report by : BBC