A climate of fear has engulfed the South African Revenue Service (Sars) to the point that some staff members are afraid to come forward to give evidence to the Nugent Commission, which is probing tax administration and governance issues at the revenue service.

This revelation came out at the opening of the inquiry which resumed on Tuesday in Pretoria.

Judge Robert Nugent, who is heading the commission, asked Sars official Dr Randall Carolissen during his presentation if he was aware that the organisation "reek[ed] of fear", and that some people were unwilling to come forward to give evidence for fear of reprisals.

"People have point blank refused to come and talk to us. I can compel them, but they remain fearful," said Nugent.

Carolissen admitted that "people have become fearful, and trust has been eroded", stating that the situation had been raised at executive level. Assurances had been given that there would be no consequences for coming forward, he said. 

He did not reveal the basis for these fears or any specific people that staff were afraid of.

Carolissen, who heads Revenue Planning, Analysis and Reporting at Sars, went on to say that the level of fear was indicative of a group suffering from a level of post-traumatic stress syndrome, due to what the organisation had gone through.

The inquiry, which began its work in June, was appointed by President Cyril Ramaphosa after he suspended former Sars boss Tom Moyane, following a breakdown of trust in his running of the organisation.

The inquiry is also tasked with probing allegations of financial misconduct at the tax service, including a shortfall of R50-billion between 2014 and 2018 under Moyane.

Nugent dismissed reports that the commission would also investigate the work or existence of the so called 'rogue unit', rejecting the suggestion as an attempt to divert the inquiry from its work.

"We are not going to bother ourselves with what a group of six people got up to. It does not form part of our work.

"If anyone feels that that they have any information of people spying on other people, they must take it to the police," he stressed. 

Other people set to give evidence include the executive for tax and customs compliance risk Thabelo Malovhele and Fareed Khan, executive for enforcement audits.

The inquiry will run until Friday, and continue for four days next week.