A statement by the ministry of state security said a terrorist group backed by the CIA and South Korea's intelligence agency had entered the country to attack with a bio-chemical substance.
It said North Korea would find and "mercilessly destroy" the terrorists.
It comes amid high tensions in the region.
The statement, carried by North Korean news agency KCNA, said the alleged plot included the use of "biochemical substances including radioactive substance and nano poisonous substance".
The Supreme Leader would have been targeted at a military parade and public procession, with the results not be visible for six to 12 months afterwards, it said.
The statement alleges that a North Korean, which it identifies only by the surname "Kim", had been "corrupted and bribed" by South Korean intelligence services while he was working in Russia.
It lists several payments made to him, and says on his return to Pyongyang he was instructed to provide detailed information about a frequently used event ground and to assess possible methods of attack.
"Korean-style anti-terrorist attack will be commenced from this moment to sweep away the intelligence and plot-breeding organisations of the US imperialists and the puppet clique," the statement says.
A war of words between the West and Pyongyang has escalated in recent weeks, with North Korea threatening to carry out a sixth nuclear test.
On Saturday North Korea conducted its second failed ballistic missile test in two weeks.
The US has sent a warship to the region and installed a controversial anti-missile defence system in South Korea.