It is reported by RIA Novosti with reference to the NHK TV channel.
The Seiryu and Koei-maru collided on the night of February 2.
The entire crew of the Koei-maru, consisting of four people, was rescued.
The Seiryu, carrying 2,200 tons of limestone, sank.
“The ship had a crew of five people, three were rescued, two more people, including the captain, were missing,” the message says.
Earlier in Japan, a Coast Guard ship ran aground.
It was also reported that the Japanese destroyer Inazuma ran aground off Yamaguchi Prefecture.