TRC advocate Robin Brink, and lawyer Ranjit Purshotum for the families, said they would oppose the application, being heard by the TRC's amnesty committee in Durban.
The three right-wingers are David Botha, 51, Adriaan Smuts, 44, and Eugene Marais, 33. Botha is serving 30 years, and the other two are serving 25 years each, for the attack.
Seven people died and 27 others were injured when the three raked a Putco bus with automatic gunfire at KwaMashu, north of Durban.
The second day of hearings on Tuesday began with testimony from surviving victims, and relatives of those who died. Eight people said their lives had changed after the attack, and many said they had lost their sources of income.
Victims like Thabani Zulu, 45, who lost his right arm, and Constance Msomi, mother of Putco bus driver Juke Constance, each told how their livelihood had been taken away.
For Botha, Louiza van der Walt said his conservative background and political beliefs at the time should be considered.
"Botha answered questions put to him truthfully (during the hearing) and I believe he is really sorry," she said.
Van der Walt and Marais' counsel, Andre Wilkins, said both men men had acted on Botha's orders.
Brink said he would strongly oppose the application.
"This was a cowardly, cold-blooded, mass murder, - nothing more, nothing less," he said.
Purshotam said the men acted against a private target and not a political opponent.
The sittings continue on Wednesday with an amnesty application by Inkatha Freedom Party member Hendrik Steyn. He was sentenced to 18 years for shooting African National Congress member Michael Mthetwa dead and wounding ANC member Simon Msweli at Kwambonambi, near Richards Bay on the KwaZulu-Natal north coast, in 1992.
A policeman at the time, Steyn was a member of the Empangeni murder and robbery unit.