The SA Revenue Service's (Sars's) head of legal, Refiloe Mokoena, who was allegedly at the centre of granting the controversial Gupta family a reported R420m VAT refund, has been suspended.

This was confirmed in the interim report by retired judge Robert Nugent on the commission of inquiry into administration and governance at Sars, released by President Cyril Ramaphosa this week.

Nugent has recommended that suspended commissioner Tom Moyane be removed and a permanent Sars commissioner be appointed to stabilise the institution. 

News reports in August indicated that Moyane had also signed off on the Gupta VAT refunds, with legal advice from Mokoena. 

In his interim report, Nugent highlighted the deep challenges plaguing Sars including turbulence among its top leadership structure — its executive committee.

Nugent said in the report that by the end of 2017, none of the executive committee members who led Sars when suspended commissioner Tom Moyane took office, remained. All members of the exco under Moyane, except two — Jonas Makwakwa and Matsobane Matlwa — had never worked for Sars before.

“None but [Makwakwa and Matlwa] had had experience of tax collection. The institutional memory that had been built up in Sars was almost entirely eradicated in exco. For completeness, Mr Matlwa, Mr Michaletos and Mr Makwakwa have since resigned, and Ms Mokoena is at present on suspension,” Nugent said.

Mokoena was asked in September to supply reasons she should not be suspended by the tax agency over the Gupta refunds. In August, Daily Maverick reported that Sars had paid more than R420m in VAT and personal income-tax refunds claimed by Gupta companies in 17 months between 2016 and April 2018.

The payments were made into a third party account, in contravention of the VAT Act, which was allegedly sanctioned by Mokoena, who provided legal advice on the matter and said she did not believe Sars needed an outside legal opinion on the matter.

Nugent’s report indicates that she has since been suspended and it is understood that she is likely to face a disciplinary process.