The investigators told Mr Kim in a letter they were advising the UN to refer North Korea to the International Criminal Court (ICC) to ensure any culprits "including possibly yourself" were held accountable.
North Korea said it rejected the investigators' report, which it called "a product of politicisation of human rights on the part of EU and Japan in alliance with US hostile policy".
The unprecedented public warning and rebuke to a ruling head of state by a UN Commission of Inquiry is likely to complicate efforts to persuade the isolated country to rein in its nuclear weapons programme and confrontations with South Korea and the West.
UN investigators said they had also told Mr Kim's main ally China it might be "aiding and abetting crimes against humanity" by sending migrants and defectors back to North Korea, where they faced torture and execution - a charge Chinese officials had rebutted.
As referral to the ICC is seen as a dim hope, given China's likely veto of any such move by Western powers on the UN Security Council, thoughts are turning to setting up some form of special tribunal on North Korea.
One UN source said: "We've collected all the testimony and can't just stop and wait 10 years."
Michael Kirby, chairman of the independent Commission of Inquiry, said the crimes the team had catalogued in a 372-page report were reminiscent of those committed by Nazis during the Second World War.
He said: "Some of them are strikingly similar.
"Testimony was given in relation to the political prison camps of large numbers of people who were malnourished, who were effectively starved to death and then had to be disposed of in pots burned and then buried. It was the duty of other prisoners in the camps to dispose of them."
The independent investigators' report listed atrocities including murder, torture, rape, abductions, enslavement, starvation and executions.
It said: "The gravity, scale and nature of these violations reveal a state that does not have any parallel in the contemporary world."
The findings came out of a year-long investigation involving public testimony by defectors, including former prison camp guards, at hearings in South Korea, Japan, Britain and the US.
Testimony to the panel included an account of a woman forced to drown her own baby, children imprisoned from birth and starved and families tortured for watching a foreign soap opera.
The abuses were mainly perpetrated by officials who ultimately reported to Mr Kim - state security, the Ministry of People's Security, the army, the judiciary and Workers' Party of Korea, according to the investigators, led by Mr Kirby.
North Korea's diplomatic mission in Geneva dismissed the findings before they were made public, saying: "We will continue to strongly respond to the end to any attempt of regime-change and pressure under the pretext of 'human rights protection'."