South African Rugby's chief executive Jurie Roux allegedly used software that masked unauthorised money transfers while he worked at the University of Stellenbosch.

Netwerk24.com says the claim is made in a report by audit firm KPMG, as part of an ongoing case in which the university - famous for its rugby history - is suing Roux in the Western Cape High Court for $3m.

Roux was a senior director of finances and asset management at the university and chairman of the Stellenbosch rugby club, before becoming the South African rugby chief executive in 2010.

It was reported last year that according to court documents, between 2002 and 2010 Roux and a colleague made "unauthorised" transfers from the university's reserve funds to cost centres which could be accessed by the rugby club.

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According to English language websites, the Afrikaans news site Netwerk24.com is now reporting that preliminary findings by KPMG show Roux "used software that would not leave an audit trail".

"The (KPMG) report reveals that Roux hid spending and withheld about R35m (NZ$3.27m)," Netwerk24 states.

"According to the audit, former Stormers flyhalf Peter Grant, former Saracens loose forward Ernst Joubert, former (Stellenbosch) coach Chean Roux and new Blue Bulls Currie Cup coach Hendré Maritz all benefited from the irregular financial management."

Netwerk24 quotes the report as stating: "Based on expert evidence and reliable interviews, it is obvious that Roux and (Chris) De Beer worked together to hide it and/or to commit a misrepresentation."

De Beer, the deputy director of student fees and Roux's successor as the Stellenbosch rugby chairman, was fired by the university in 2012.

Roux's lawyer said there would be no comment on the latest allegations because of his legal battle with the university.

Last year, Roux confirmed he was interviewed by the university and said: "There was no suggestion of personal gain. I deny any wrongdoing."

Roux was given a five-year extension to his South African rugby CEO contract in 2014.

At the time, president Oregan Hoskins said: "We were made aware of certain allegations and we have interrogated them. We are satisfied with the explanations that Jurie Roux has given to us.

"It is gratifying that, despite all the publicity, the 14 member unions of SARU voted unanimously to approve Jurie's reappointment."