The files that vanished after SAPS general’s murder

Two SAPS officers — one of them a former head of crime intelligence — have been raided by police in connection with allegations that they removed sensitive files, including those linked to an investigation into the Phala Phala case, from a murder scene.

Former top cop Mulangi Mphego and Sgt Ishmail Phungu are alleged to have personally authorised the removal of investigative files without any chain of custody, there was no SAPS 13 receipt acknowledging evidence has been taken or an entry in a pocketbook.

The claims relate to the murder of Lt-Gen Sindile “Pitso” Mfazi at his home in July 2021. The raid, conducted last month, was carried out by the police’s cold case unit. Phungu was Mfazi’s former close protector.

At the time of his death, Mfazi was probing the fallout from the February 2020 burglary at President Cyril Ramaphosa’s Phala Phala farm.

He was not investigating the theft of the foreign currency itself. According to a protected disclosure submitted to parliament in March, his inquiry focused on allegations that crime intelligence funds and state resources were unlawfully diverted to run an off-book covert operation to track the Phala Phala thieves and contain the political fallout.

Mfazi was also probing the murder of Western Cape senior detective Lt-Col Charl Kinnear, who was assassinated outside his home in September 2020. Several suspects are on trial for his murder, including alleged underworld gang leader Nafiz Modack.

In his official pocketbook, Mfazi entered a highly detailed calls log, dated November 22 2020, in which he meticulously documented his telephonic tracing of the docket relating to the circumstances surrounding the killing.

While the motive for Mfazi’s murder is unknown, these two cases provide a hint as to why anyone might have wanted him dead. It is unclear what last month’s raid uncovered.

The explosive claims against Mphego and Phungu are contained in an affidavit supplied to police by a former associate of Mfazi, who was at the scene after his death.

Mphego and Phungu are also alleged to have ordered the destruction of digital evidence by wiping Mfazi’s cellphone at the scene.

The affidavit questions why Mphego — who was also a special adviser to former deputy president David Mabuza — was even at the murder scene.

While the SAPS initially maintained that Mfazi, the deputy national commissioner for crime detection, had succumbed to a Covid-related illness, subsequent forensic investigations involving exhumation and toxicology results revealed that he had actually been poisoned.

The associate’s affidavit states: “General Mphego, a man with no lawful command over the [SAPS], nonetheless assumed control of the scene, instructed me to prevent the general’s own wife from entering her home ... ordered the destruction of digital evidence by wiping the general’s cellphone, and personally authorised the removal of sensitive investigative files without any chain of custody, without any SAPS 13 receipt, and without any entry in any pocketbook.”

However, Mphego this week denied entering Mfazi’s home or taking files on the day of his death or in the days that followed.

“Pitso was my friend. I am not involved. I was outside [the house]; I was scared to enter that house because of Covid. If they say I entered the house, they need to tell me when and what date because everything was taken away by [Mfazi’s] family,” Mphego told the Sunday Times.

Attempts to contact Phungu were unsuccessful.

The 2020/21 Secret Services Account records that what Mfazi flagged as “missing” during his audit were the exact files needed to prove the unlawful expenditure he was investigating. The missing records are considered the primary files needed to verify the alleged unauthorised spending.

According to the associate’s affidavit, when they entered Mfazi’s house on the day of his death, papers bearing the letterheads of the SAPS, the public protector and the National Prosecuting Authority were scattered across the lounge table in complete disarray. Upstairs, they found the general’s body with blood stains emanating from his nose and some on the walls.

The associate said he met Phungu at home affairs to secure the death certificate on July 9. He said Phungu, who had spent the early hours with sole and unrestricted access to Mfazi’s Pretoria residence, used the general’s bank cards to withdraw cash, handing him R1,600 for fuel. He then handed the associate several of Mfazi’s personal belongings, including his bank cards, wallet and house keys. Among these items was Mfazi’s iPhone.

The phone, however, was entirely blank. The associate noted that it was “an iPhone cellphone which belonged to Mfazi. This cellphone was switched on and it had been wiped clean, according to Sgt Phungu.”

“He informed me that Gen Mphego had instructed him to ensure that it is reset to factory default settings and all data removed,” the associate said.

But Mphego denied issuing such an instruction. “I am no longer serving. I could not have instructed Phungu to wipe a phone,” he told the Sunday Times.

The destruction of evidence was not limited to digital data. According to the affidavit, on the morning of July 14, as the family prepared to fetch the Mfazi’s remains from the mortuary, Phungu arrived at the gate at 4.30am demanding a “specific file”.

When the associate hesitated and pressed him for details, Phungu called Mphego, who “directly instructed me to assist Sgt Phungu immediately”.

“Phungu went straight to a box of investigative files and removed the document. No chain of custody was recorded, no SAPS 13 receipt was issued, and no entry was made in any pocketbook,” the associate said.

Reflecting on these events, the associate said he realised that the alleged actions of Phungu and Mphego were part of an alleged co-ordinated effort to bury the truth.

“The active management of the aftermath by Sgt Phungu, Gen Mphego and the others with direct political interests in the investigations Gen Mfazi was pursuing leaves me with only one conclusion, which I state without hesitation under oath: they were not merely present at the scene of a dying senior officer — they were executing a premeditated operation to seize and suppress evidence.”

Mfazi, according to his pocketbook, also exposed the staggering scale of corruption during the pandemic. On December 15 2020, Mfazi chaired an internal audit meeting reviewing the procurement of emergency Covid-19 personal protective equipment (PPE).

He documented a vast procurement universe of R1.6bn, flagging systemic governance failures, including verbal approvals without written authorisations; payments processed without stock controls; and an estimated R35m in direct irregular losses.