The 29-ton fishing boat 3 Dae Kyong was carrying a crew of seven Koreans and two Indonesians. Two Koreans were rescued immediately after the collision by the crew of the cargo ship, four bodies were found in the overturned vessel by Korean divers, and the final three remained unaccounted for Sunday, Japan's coast guard said.
No one on the 3,843-ton cargo ship, the Joshu Maru, was injured, it said.
Japanese and South Korean ships and aircraft were searching the area Sunday for the missing crew members.
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