A coastguard spokesman told AFP that the bodies of two North Korean sailors had been recovered and three other crew had been rescued, with 11 still missing.
The 4,300-tonne Mongolian-flagged ship sent out a distress call shortly after 1:00 am (1400 GMT Thursday) from international waters off South Korea.
The boat, with a cargo of iron ore and copper powder, was sailing from North Korea to China on a sea route regularly used by North Korean cargo ships.
The three rescued sailors were taken to a hospital on the southern resort island of Jeju.
"Our operation has been hampered by strong winds and high waves," Kim Sang-Bae, the coastguard chief in Yeosu, told a televised news conference.
A coastguard helicopter found a surviving sailor drifting in the sea about three hours after the distress call came. Two crew members were rescued later.
Officials said Japan's coastguard had been asked to join the operation.
They said they would question the survivors to identify the cause of the accident.
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