Addressing several thousand African National Congress supporters at a commemoration service Mandela said that there are still those who continue to bury their heads in the sand.
"They have failed to shed their party political preoccupation and put the country first.
"They have not called on their erstwhile employees to come clean and co-operate with the commission. They claim they did not know, and they expect South Africa and the world to believe them."
Former state president and National Party leader FW de Klerk has repeatedly denied any knowledge of atrocities committed under the former regime.
Without naming anyone, Mandela said: "The people who led apartheid cannot avoid accepting responsibility for acts which were seen as crimes in the eyes of the entire world.
"The time is now for those who led the country into the political wilderness to admit the error of their ways.
"I wish to take this opportunity, as president of South Africa, to call on all political parties and organisations, on all soldiers and others across the old political divide - on all among these and other forces who have reason to apply for amnesty - to do so before the 10th of May."
Former SA Defence Force chiefs on Saturday said former soldiers should not apply for amnesty for cross-border raids.
Mandela was speaking at a commemoration service to honour five Umkhonto we Sizwe operatives who went missing in 1988 and 1990.
They were Charles Ndaba, Mbova Mzimela, Bheki Mkwhanazi, Mbuso Shabalala and Phila Portia Ndwandwe.
The skeletons of Ndwandwe and Mkhwanazi were found in a shallow grave in the Elandskop area near Pietermaritzburg in March.
Mzimela's remains were exhumed on a farm on the north coast.
Vula operatives Ndaba and Shabalala's corpses were weighted and thrown into the Tugela River in 1990.
Operation Vula sought to establish an underground ANC structure in South Africa before the elections in 1994.
A group of former security policemen confessed to the TRC to killing the five and pointed out where they had been buried.
On Saturday morning five coffins covered in the colours of the ANC lay in state in the Currie's Fountain sportsground.
Family members of the victims were seated under a marquee in the grounds.
Ndwandwe's only son, Thabang, 9, was one of several family members to receive service medal awards handed over by Mandela and deputy defence minister Ronnie Kasrils.
The activists' remains were reburied in the Chesterville cemetery north of Durban on Saturday afternoon.