Kim visited military detachments on two islets controlled by North Korea on Friday (5 May), while forming a strategy against the "South Korean puppet army", state media reported.
NKNews.org reports that the intelligence agencies are accused of attempting to carry out a biochemical attack against the leader during North Korea's April 15 military parade, which celebrated the 105th birthday of DPRK founding leader Kim Il Sung.
The ministry said the spy agencies "ideologically corrupted and bribed" a North Korean citizen who had been working in Russian Federation to carry out the alleged assassination attempt involving a "radioactive" and "nano-poisonous" substance.
The ministry 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 Russian Federation.
The claims come amid high tensions in the region.
KCNA laid out the alleged plot in great detail, saying it was hatched in 2014 when the South Korean and USA intelligence agencies recruited a North Korean working in the timber industry in eastern Russian Federation.
The CIA and Seoul's Intelligence Services have "hatched a vicious plot" involving unspecified "biochemical substances" to kill the hermit state's young leader during public ceremonial events in Pyongyang, the Ministry of State Security said.
Secretary of State Rex Tillerson has said that the administration is not seeking regime change in North Korea, and he told ABC last month that he was "not aware" of any plans to assassinate Kim.
The KCNA report did not say when the assassination plot was stopped.
The US has sent ships and engaged in military exercises along the Korea border.
North Korea frequently lambasts the United States and South Korea, but this accusation is unusual in its details.
Recent tests by North Korea have drawn global condemnation, with Beijing becoming increasingly frustrated itself at these test and have shown no opposition to increased sanctions.
North Korean leader Kim Jong Un provides field guidance at the construction site of Ryomyong Street in this undated picture provided by KCNA in Pyongyang on March 16, 2017.