The Yonhap news agency quoted Lee Jae-joung, the country's unification minister, as saying: "It's about how we can prevent conflict and make the area more productive, while leaving the NLL unaffected, and the government has never had the intention to change or get rid of the NLL," adding that he thought North Korea shared the view.
The statement was made to ease tensions in South Korea caused by President Roh Moo-hyun's recent speech, where he said the NLL was a redline for South Korean ships rather than an official border.
At the historic second summit of the Korean leaders held in October both sides agreed to establish a joint fishing zone and arrange a meeting between the countries' defense ministers in November.
The maritime demarcation line (NLL) was drawn up by the United Nations after the Korean War of 1950-1953, but has never been recognized by the Communist state, which is calling for it to be moved further south.
The border dispute has caused a number of clashes in the area. The latest occurred in the summer of 2002, when six South Korean naval officers were killed and 18 injured, and in 1999, the South Korean Navy sank a North Korean vessel killing some 30 sailors.