The National Prosecuting Authority (NPA) has denied responsibility for failing to investigate and prosecute around 300 apartheid-era cases, as recommended by the Truth and Reconciliation Commission (TRC), blaming political interference from former president Thabo Mbeki’s government.

The NPA’s admission is contained in court papers in the case against former security branch policeman Joao Rodrigues, charged for the 1971 murder of Ahmed Timol.

“I do not deny that the National Prosecuting Authority was subjected to political interference and political pressure not to immediately prosecute cases such as the present,” said Jacobus Petrus Pretorius in an affidavit signed on Monday on behalf of the NPA.

Pretorius cited testimony from former NPA boss Vusi Pikoli, senior deputy director of public prosecutions in the Priority Crimes and Litigation Unit (PCLU) Raymond Macadam, and former PCLU boss Anton Ackermann.

“The (NPA) does not deny that the executive branch of the State took what one can describe as political steps to manage the conduct of criminal investigations and possible prosecution of the perpetrators of the political murders such as that of Mr Timol,” said Pretorius.

Timol, an anti-apartheid activist, was tortured and pushed off the 10th floor of John Vorster Police Station (now Johannesburg Central Police Station) by security branch officers. In 2017 his family finally convinced the NPA to reopen of the inquest into his death, which overturned the finding from suicide to murder.

Many such families have questioned why the police and NPA have failed to investigate and prosecute hundreds of similar cases.

In his affidavit, Macadam describes how former Scorpions’ director Malala Geophrey Ledwaba in 2003 placed a moratorium on investigating TRC cases. A task team established to handle the issues was stacked with intelligence officers and seemed more concerned about why the cases were targeted rather than taking them forward.

Macadam said he tried multiple times to prioritise TRC cases over the years but there was no support from his bosses.

In 2017, former NPA head Shaun Abrahams asked him to collect Pikoli’s documents from a strongroom. Macadam found multiple documents suggesting former president Thabo Mbeki’s government was considering measures to prevent prosecuting those who had not applied or were denied amnesty at the TRC.

They included a second draft of an Indemnity Bill allowing the president to grant indemnity for politically-motivated crimes committed from 1960 and a report from the task team on whether private prosecution and civil litigation can be avoided if the NPA decides not to prosecute such cases.

Most damning, Macadam found Pikoli’s now well-known 2007 correspondence with former justice minister Brigitte Mabandla. She expressed her concern after hearing the NPA planned to prosecute TRC cases.

In a secret memorandum, Pikoli replied: “I have now reached a point where I honestly believe that there is improper interference with my work and that I am hindered and/or obstructed from carrying out my functions on this particular matter. Legally I have reached a dead end.”

Pikoli was certain his decision to open apartheid-era cases played a role in his suspension, possibly because ANC members could have been charged alongside apartheid officials. An internal Scorpions memo from 2003 said the TRC denied amnesty to 37 high-ranking ANC officials.

“What one sees in Pikoli and Ackermann’s affidavits is that the political interference and political pressure brought to bear upon the highest office of the National Prosecuting Authority was far from being authorized by law,” Pretorius said this week in his affidavit.

Former TRC commissioners on Tuesday wrote to President Cyril Ramaphosa asking him to establish a commission of inquiry into political interference in prosecuting TRC cases. The TRC report called for “a bold prosecution policy”.

The commissioners said: “Both the SAPS and the NPA colluded with political forces to ensure the deliberate suppression of the bulk of apartheid-era cases. Even though the TRC had handed over a list of several hundred cases to the NPA with the recommendation that they be investigated further, virtually all of them were abandoned. All these cases involved gross human rights violations such as torture, murder and enforced disappearances in which amnesty was either denied or not applied for (the TRC cases).”

The commissioners called on Ramaphosa to apologise to apartheid victims and bring the masterminds of violence to book: “While junior officers must face justice, they acted at the behest of the generals and politicians who remain shielded from accountability. The failure to pursue those most responsible speaks volumes about the captured state of our criminal justice system.”

On behalf of Police Minister Bheki Cele, in court papers Colonel Mabina Mahlangu denied claims that SAPS had failed to investigate TRC cases, saying “the criticisms levelled against the DPCI and the National Prosecuting Authority is intended to unnecessary negative publicity”.

Justice Minister Michael Masutha’s court papers did not touch on who is responsible for the failure to prosecute TRC cases.

Mahlangu said the Directorate for Priority Crime Investigation, better known as the Hawks, received a batch of TRC cases to investigate in 2010 and another 20 cases in 2018. Fifteen officers have been assigned to investigate.

The Ahmed Timol case will resume on 28 March in the South Gauteng High Court to hear Rodrigues’ application for a permanent stay of prosecution. The NPA, Masutha and Timol’s nephew Imtiaz Cajee have all opposed the application. DM