Three people died in events and eight were still missing the call on Sunday morning.
Ko Jae-young, an officer of the Coast Guard, said 11 South Korean sailors and five Burmese colleagues were on the ship of 419 tons when the explosion was heard. He had no information as to what caused the blast.
Mr Ko said five sailors were rescued and emergency services were at work to try to locate the missing.
The Coast Guard said the ship was carrying chemicals normally, but it was empty when it sank.
The explosion occurred relatively far from the sea border between South Korea and North Korea, a politically tense. The Coast Guard said there was no evidence that Pyongyang was involved in these events.
North Korea was accused of having torpedoed a battleship South Korea in 2010, killing 46 sailors. Pyongyang has denied any involvement.