Coast guard official Kim Yong-jin says that the fire broke out on the 1,400-ton ship early Friday in waters off the country's southeastern port of Busan.
South Korean authorities dispatched two vessels to the scene and put out the fire in 70 minutes.
Kim said the empty Cambodia-registered cargo ship, Yunxing, was carrying a crew of eight Chinese and one from Myanmar.
Kim said coast guard officials plan to question the five survivors on the cause of the fire.