The 76-tonne fishing boat Daifukumaru capsized in the Sea of Japan just off Shimane prefecture at about 5:20 am, leaving all nine crew on board missing, a Japan Coast Guard spokesman earlier told AFP.
Coast guard rescuers on a helicopter spotted a man floating with his face down five hours after the accident and took him to hospital where he was confirmed dead, another spokesman said.
Patrol boats and aircraft are continuing to search for eight other men still missing, he added.
The nine crew members include eight Japanese and one Indonesian.
The nationality of the man discovered has yet to be confirmed, according to coastguard officials.
"They were fishing for crabs when water flowed into the boat," an official with the local fishermen's union that operated the vessel said on public broadcaster NHK.
"So the boat was towed by another vessel. That was when it capsised."