Pham Minh Tuan was found by police in Jolo, believed to have been executed by his Abu Sayyaf captors led by Indang Susukan, a bandit wanted by the Eastern Sabah Security Command (Esscom).
Pham was the skipper of the Vietnamese vessel MV Royal 16 hit by an Abu Sayyaf group near the island province of Basilan last November.
Pham’s remains were exhumed on Friday, said chief superintendent Graciano Mijares of Mindanao police regional office.
“This was an initiative of the Sulu provincial police, the Joint Task Force Sulu and the Mindanao field unit of the Anti-Kidnapping Group,” Mijares was reported as saying.
The Vietnamese is believed to have been killed during clashes with the army in Talipao town in Sulu.
“His body was possibly buried in Jolo, the capital of Sulu, to mislead the authorities,” Mijares said.
The Abu Sayyaf bandits are suspected to have held Pham in Basilan province before he was moved to Sulu due to pressure from armed villagers.
A source in Esscom told FMT that Indang is wanted by the Malaysian authorities for cross-border crimes at sea.
“We are constantly in contact with our Philippine counterpart with regard to latest intelligence on Indang and his gang of bandits,” the source told FMT.
Pham was kidnapped along with five crew members of the ship before the pirates fled with the captives in a speedboat.
The five crew members had earlier been killed or had escaped.
Hoang Vo, 22, escaped from his captors and was rescued following an airstrike that targeted the hideout of Abu Sayyaf sub-leader Furuji Indama on June 16.
Hoang Trung Thong and Hoang Van Hai were beheaded and their remains were found in Sumisip town, Basilan province, on July 5.
A bullet-riddled body believed to be that of Tran Khac Dung was found by the military on July 8 in Patikul town, Sulu province, while Do Trung Huie was rescued on Mataja island in Basilan in August.
The hijacking of the ship was reported to have come a few days after a warning that slow-moving ships with low freeboard should reroute away from the southern Philippines as attacks in the area had increased.