“Our divers found all the bodies of the missing 12 crew members inside the ship,” a coast guard official told AFP.
Japanese authorities later said one of four crew members who had been rescued from the fishing boat subsequently died, bringing the death toll to 13.
Thursday’s collision occurred 400 kilometers (250 miles) north of the Oki Islands in the Sea of Japan, also known as the East Sea.
The Chinese vessel, the 290-ton “Lurong Yuanyu 378,” had 16 Chinese-national crew members in total.
The Hong Kong-flagged ship was identified as “Brightoil Lucky,” a 63,294-ton tanker carrying 21 crew members.
The tanker’s crew were believed to be safe.
Japan had deployed three patrol boats to search for the missing crew, after responding to a plea for help from their Chinese counterparts.