The Mongolian-flagged ship -- with a South Korean captain, and two South Korean and 18 Indonesian crew members -- successfully outdistanced a suspicious boat that had pursued it for more than an hour in an apparent attempt to capture it, the ministry said in a statement.
The ship had raised the alarm that it was being chased before contact was lost, prompting a South Korean anti-piracy naval ship in the area to sail to its rescue.
Somali pirates hijacked an Iranian fishing boat with a crew of up to 20 on Tuesday. There have been at least eight attacks by Somali pirates in recent months and three successful hijackings.
Last week the Indian navy thwarted an attempted hijacking, chasing away at least three boats that had swarmed a cargo vessel off Somalia's northeast.
Lawlessness and a lack of job opportunities in Somalia, combined with the waning attention of international anti- piracy patrols has given piracy new life.