In 2013 the Philippines apologised to Taiwan over the killing of a Taiwanese fisherman by Filipino coastguards who said his vessel had illegally sailed into local waters.
Immediately after receiving the report, the ministry instructed the Vietnamese Embassy in the Philippines to contact the departments of Foreign Affairs and National Defence of the Philippines to verify the information and take appropriate measures to protect the citizens.
The Philippine government has promised Vietnam a "fair and thorough" investigation into the deaths two of its fishermen following an encounter with the Philippine Navy on Saturday.
The Filipino navy personnel "followed the rules of engagement, including identification protocol and use of radio and public address system", the official said, adding that the Vietnamese fishing boat was towed to Pangasinan after the incident.
The Philippine DFA said it received reports that Saturday's incident involved a Navy patrol vessel and six Vietnamese fishing boats that it encountered in sea areas near north of Luzon island, and the Navy patrol boat went after the Vietnamese fishing vessels, suspecting of illegal fishing.
Officials are investigating the cause of the pair's death, but their bodies were found after a Vietnamese boat slammed into the Philippine vessel, said Lieutenant Jose Covarrubias.
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"The six fishing vessels fled but one maneuvered and hit the Philippine navy ship, prompting its crew to fire warning shots during the commotion", the official said, adding that two Vietnamese fishermen were later found dead and five others were arrested.
Five other fishermen were reportedly arrested for intruding into Filipino waters during the incident.
The security official told AP the Vietnamese vessels were using powerful lights to attract fish off Bolinao town.
That incident triggered a diplomatic spat, with Taiwan suspending the hiring of Philippine workers and recalling its envoy to Manila in protest.
The use of such fishing accessory, known locally as "superlights", is prohibited under Philippine law.
Vietnam and the Philippines have both voiced opposition to China's assertions of its territorial claims in the South China Sea, but Philippine President Rodrigo Duterte has toned down his country's criticism in an effort to thaw once-frosty relations and revive trade with Beijing.