President Cyril Ramaphosa is setting up a judicial commission of inquiry to establish whether attempts were made to prevent the investigation or prosecution of apartheid-era crimes, his office said on Wednesday.

The move is the outcome of settlement discussions in a court case brought by families of the victims of political killings and disappearances that happened decades ago, who say post-apartheid governments never properly investigated those crimes.

"Allegations of improper influence in delaying or hindering the investigation and prosecution of apartheid-era crimes have persisted from previous administrations," the presidency said in a statement.

"Through this commission, President Ramaphosa is determined that the true facts be established and the matter brought to finality."

After apartheid ended in 1994, South Africa set up a Truth and Reconciliation Commission (TRC) to help uncover human rights violations perpetrated under white minority rule.

The TRC handed over a list of several hundred cases to State prosecutors for investigation, but many were never pursued.

The 25 family members and survivors who filed the case in a Pretoria court in January are also seeking about R167-million from the State in damages.

The government will ask for their application to be suspended pending the commission's findings, the presidency said. It did not give a time frame.

The Foundation for Human Rights, an NGO supporting the families, said that they welcomed the establishment of a commission of inquiry but opposed the president's move to delay a ruling on their damages claim.

"Instead of entering into mediation, he has decided to offload the declaration of rights and constitutional damages onto a commission of inquiry, which has no authority to deal with it," it said in a statement.