Thomas Hammarberg, the UN's special representative for human rights in Cambodia, said people had to understand there should be no immunity in such matters.
His comments came after Cambodian Prime Minister Hun Sen rejected calls by human rights groups for the two men to stand trial for crimes against humanity.
The men, Khieu Samphan and Nuon Chea, are having talks with Hun Sen at a military base just ouside the capital Phnom Penh after leaving their base in the western town of Pailin.
'Bury the past'
Hun Sen said Cambodians should "dig a hole and bury the past and look to the future".
He said a trial might cause a return to civil war and that the Phnom Penh government should be allowed to decide how to deal with the last remnants of the Khmer Rouge.
![[ image: width=150]](/olmedia/240000/images/_243634_hunsen150.jpg)
Until recently the prime minister had said he fully supported the establishment of a tribunal to prosecute key Khmer Rouge leaders for crimes against humanity.
Human rights groups say that there can be no reconciliation in Cambodia until leaders of the guerrilla movement are held accountable.
Our correspondent in Phnom Penh says that view is shared by many ordinary Cambodians, who believe that those who wielded power should stand trial for their part in allowing the deaths of more than one million innocent people.
After the men surrendered on Christmas Day, Hun Sen hinted that they might be pardoned.
His comments were echoed by Cambodia's monarch, King Sihanouk, who expressed his deep gratitude that the men had surrendered.
However, Sidney Jones, director of Human Rights Watch Asia, said it was unthinkable to allow the men to return to society as if one of the worst massacres of the 20th century never took place.
Key figures
Khieu Samphan was the group's nominal leader in the 1980s, while Nuon Chea was a shadowy figure who devised much of the Khmer Rouge's extreme left-wing ideology.
Their emergence means the only senior Khmer Rouge commander still on the loose is Ta Mok, a lieutenant of the reviled dictator Pol Pot, who died of a suspected heart attack in March.
![[ image: width=150]](/olmedia/240000/images/_242577_samphan.jpg)
Khieu Samphan became the public face of the secretive Khmer Rouge when he represented the movement during 1991 peace talks.
He was officially head of state in Cambodia between April 1976 and the overthrow of the guerrillas by the neighbouring Vietnamese in 1979.
In that period, later documented in the Oscar-winning film the Killing Fields, an estimated 1.7 million Cambodians died through disease, starvation or execution.
Nuon Chea, 71, was the official number two to Pol Pot.
Khieu Samphan and Nuon Chea have come forward two years after the defection of top Khmer Rouge cadre Ieng Sary, which coincided with a fatal split in the movement.
The last Khmer Rouge fighters surrendered to the government earlier this month.
Khmer Rouge leaders surrender
(26 Dec 98 | Asia-Pacific)
Letters of surrender - full text
(29 Dec 98 | Asia-Pacific)
Cambodia's troubled history
(21 Jul 98 | Asia-Pacific)
Architect of the 'killing fields' escapes justice
(16 Apr 98 | Asia-Pacific)
Legacy of the Khmer Rouge
Background to the Khmer Rouge regime
Cambodia Web
The Cambodian Genocide Programme
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