The incident happened on Monday off Basilan province, a stronghold of Muslim rebels.
Three other men were 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.
Police say that about 10 attackers are suspected of involvement in the incident.
The fishermen were aboard three wooden vessels off Sibago island in Basilan when gunmen in speedboats opened fire.
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