The trio two Chinese and one from Myanmar were part of a group plucked from chilly waters in the strait separating Japan's main Honshu and northernmost Hokkaido islands.
They were initially listed as "unconscious".
"They were sent to hospital where they were confirmed dead," a local coastguard official said.
The 10 crewmen abandoned the ship just before it sank.
Among the seven other crew members are two Bangladeshis, including the captain, and five Chinese. They are in a stable condition.
