Divers found a body in the ship's hold yesterday and it was later confirmed as that of captain Masaichi Ando by his family, the coastguard said.
Ando, 64, had been missing since the nearly 1,000 tonne tanker, Shoko-maru, erupted in a fireball on Thursday.
It went down around 10 hours after the blast.
Seven of the eight Japanese crew were rescued, including one who remained unconscious with severe burns covering his entire body.
The fire was likely sparked as a crew member used a grinder to remove rust on the ship, Transport Minister Akihiro Ota told a press conference last week.