The visit is part of talks involving six countries - the two Koreas, the U.S., Russia, China and Japan - under a deal providing fuel and economic incentives to North Korea in exchange for Pyongyang giving details of its nuclear program and disabling its atomic facilities. The process recently came to a halt amid diplomatic wrangling.
South Korea, which has 20 nuclear reactors providing the country with 40% of its energy needs, will send six nuclear experts to Pyongyang via Beijing headed by South Korea's chief nuclear envoy Hwang Joon-kook, Yonhap said. It his hoped the visit may provide an impetus to the stalled talks.
"Our fact-finding team will focus on the technical and economic aspects of a decision on the handling of North Korea's unused fuel rods," the ministry said in a statement.
Seoul said that North Korea had fulfilled eight out of 11 points of its obligations to disarm its nuclear reactor in Yongbyong, 100 km (62 miles) north of the capital, Pyongyang. North Korea still needs to remove all the unspent fuel rods from its nuclear plant and dismantle its transportation system.
Last year, North Korea announced that it had 14,000 unspent nuclear fuel rods, which South Korea estimated contained 100 tons of uranium. So far 5,500 spent rods have been removed out of the total of 8,000 that were stored at the Yongbyong nuclear facility. Every day 15 more rods are removed.
Relations between Seoul and the communist north have deteriorated since South Korean President Lee Myung-bak took office in February 2008, and amid claims that North Korea's leader Kim Jong-il has been incapacitated following a stroke in August.
The leader is not known to have appeared in public since he missed a major anniversary parade in August, but North Korean state media frequently release photos purportedly showing him paying various visits around the country.
Relations between the two sides were dealt a further blow last month, when the North tightened controls on the heavily fortified border, and expelled some of the South Koreans working at the Kaesong industrial park, close to the border.
Each of the five countries, involved in the talks, agreed in 2007 to give the North 200,000 metric tons of fuel oil as an incentive for North Korea's nuclear decommissioning and disclosure of all information on past nuclear activities. The move followed a nuclear test blast conducted by the communist state in October 2006.