"The joint investigation team of police and prosecutors asked for warrants to arrest three crew, including the captain," the official in the southern coastguard headquarters in Mokpo told AFP.
The request was submitted to the local court, he said, while adding that he was unaware of the precise charges.
The captain and most of his 28 crew managed to escape the ferry, and have been criticised for abandoning the ship when so many were still trapped on board.