"The official was abducted when he got off work. No further details, including the whereabouts and motive of the abduction, are confirmed yet," Xinhua quoted a ministry official as saying.
The trade official was kidnapped by four unidentified armed men on his way home after work in Libya's capital city Tripoli Sunday, the foreign ministry official said.
The abducted official was identified as Han Seok-woo, head of the Libyan unit of the Korea Trade-Investment Promotion Agency (KOTRA). Han, 39, has worked in the Tripoli office since July 2012.
It was the first time that a South Korean has been abducted in Libya, where public security is in a poor state.
Since the ouster of Libya's long-time leader Muammar Gaddafi in 2011, the country remained in shambles despite efforts to quell rising lawlessness.
South Korea will issue a special travel warning on Monday afternoon to prevent its citizens from travelling to the North African country due to the abduction case, the ministry official said.