The intelligence organisation sent him back to the North after training him to gather information about Kim's official visits.
"The organisation also sent him speech and acoustic sensing and pursuit devices for tracking the movement of the top leader and even violent poison," the statement said.
"This case goes to prove that the South Korean puppets have gone the lengths of resorting to thrice-cursed methods to dare harm the headquarters of the DPRK, hell-bent on inciting confrontation with the DPRK."
North Korean officials have said relations with the government of Lee Myung-Bak, the South Korean president, have "reached an extremely dangerous phase".
North and South Korea have tried to kill each other's leaders during the Cold War era, but there have been no known attempts since 1983, when a North Korean bomb in Yangon, Myanmar missed Chun Doo-Hwan, the then-president.
Seoul's unification ministry has declined to comment on the claim, which comes at a time of increasingly tense relations between the North and South.
The North expelled hundreds of South Korean workers from the Kaesong joint industrial estate earlier this month and imposed strict border controls in protest at what it called Seoul's "confrontational policy".