The agent has been detained since June, when he entered South Korea posing as a defector, the Yonhap news agency reported.
The man, surnamed Kim, confessed during his interrogation that he was a spy for North Korea's National Agency. He said while he was conducting espionage activities in China in July 2010, Pyongyang ordered him to assassinate Kim Jong-nam, the half-brother of North Korean leader Kim Jong-un.
The oldest son of the late Kim Jong-il lost favor with his father after he attempted to enter Japan in 2001 with a fake passport.
The spy was unable to carry out his assignment. Kim Jong-nam was reported in February to be living in Macao.
Kim, the spy, said he entered South Korea to report on the large number of defectors living there. He was instructed to approach Park Sang-hak, a defector who often launches balloons carrying anti-North Korean leaflets into the communist state.