A spokesman for the State Security Ministry said in a statement on national TV: "Recently, a person surnamed Ri was discovered and arrested while preparing to carry out a terrorist mission on orders from a South Korean puppet intelligence organization to do harm to the safety of the top leader of the DPRK [North Korea]."
The spokesman said the suspect had been given hi-tech equipment to track Kim's movements, as well as deadly poison.
The claim comes amid worsening relations between the two neighbors and widespread rumors that Kim Jong-il has been incapacitated since suffering 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.
The South Korean government has not yet responded to the assassination claim.
North-South relations were dealt a new blow earlier this 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.
Ties have deteriorated since President Lee Myung-bak came to power in South Korea in February. The new president has demanded more progress in the North's denuclearization in return for the economic support provided by the South.