"The Constitutional Court... has not stopped the sitting from going ahead on Monday," she told Sapa.
The Azanian Peoples' Organisation and families of four slain anti-apartheid activists this week asked the court to rule on the constitutionality of legislation establishing the Truth Commission.
They said amnesty provisions in the Promotion of National Unity and Reconciliation Act were in conflict with the constitutional right to redress for past wrongs.
Nienaber said the respondents, President Nelson Mandela, Justice Minister Dullah Omar, Safety and Security Minister Sydney Mufamadi, the commission and the government of national unity, had three days to file notice that they would oppose the application.
They would then have ten days to file their heads of argument before the court considered whether the families had grounds for their application.
The commission is preparing to hear testimony of alleged torture, murder and disappearances from 28 apartheid victims during its historic first hearings starting on Monday,