Those who confessed to the commission could seek amnesty for their crimes, but some chose not to.
Vlok, 79, appeared before the truth commission but did not seek amnesty for the 1989 attack on Reverend Frank Chikane, now an adviser to Thabo Mbeke, the president.
Vlok and Chikane appear to have made peace. In an act mimicking Jesus Christ, Vlok even washed Chikane's feet and the two men have prayed together.
But while Chikane says he has forgiven Vlok, he says he cannot stop the court process.
Many feel that Vlok, who was security minister from 1986-1989, when an estimated 30,000 people were detained, should not be standing trial.
Antjie Krog, an author and academic, said: "I feel they should have focused on the people who didn't participate in the [reconciliation] process, instead of going for a soft target. What kind of message are you sending, 'if you came forward it will just continue'?"
But others say the trial should been seen as another step towards reconciliation.
Zweli Mkhize, who says he was tortured by the white security forces, said: "Vlok and his like must face justice for the atrocities. How can there be reconciliation when there is no justice?"
Vlok's trial is also turning the spotlight on de Klerk, who became president in 1989 and helped usher in black majority rule.
There has been speculation that Vlok and Van der Merwe may have reached a plea bargain deal with prosecutors, possibly implicating de Klerk.
De Klerk says he knew nothing of any atrocities and recently said that if there were to be any further prosecutions, former African National Congress (ANC) guerrillas should be brought to book along with members of the white security forces.
Although the vast majority of atrocities were committed by white security forces, ANC guerrilla forces waged land mine and bombing campaigns in which civilians died.
Among those were Kobie van Eck and her two children, aged two and eight, who died with three of their friends when their vehicle hit a mine laid by the ANC's military wing in 1985.
The two men involved were sentenced to life imprisonment but then given an amnesty by the Truth and Reconciliation Commission.
Dirk van Eck, who survived the attack, is now lobbying for the ANC leaders who authorised the land mine campaign to be brought to justice.
Kallie Kriel, head of the white-dominated AfriForum organisation, which plans to demonstrate outside Pretoria's High Court where Vlok's trial is taking place on Friday, said: "Not treating the ANC leaders in the same manner, will amount to selective morality."