Eye Witness News (EWN) have reported that investigations are currently underway to study claims that certain teams are fielding ineligible players.
Eyewitness News Sport understands three teams are facing charges, with a further three under suspicion in the Varsity Shield.
It is alleged they were fielding players that were not registered as varsity students, while falling short of the required 16 student players.
Nelson Mandela Metropolitan University has been cleared of any wrongdoing.
The other two teams, Tuks and Shimlas, may be cheating according to a source which claimed auditing firm Deloitte backed the findings.
On Thursday, a disciplinary hearing was also held.
A memorandum from Varsity Cup CEO Duitser Bosman was circulated to all 13-member varsities to inform them of the investigation.
Bosman said he could not comment on the matter as yet.
(Edited by Zethu Zulu)