Walter Sisulu University (WSU) and the University of Fort Hare (UFH) were cited among historically disadvantaged universities to face the review.
The two universities could benefit from additional funding from the Department of Higher Education and Training (DHET) if they meet the required criteria, which include submitting a business plan outlining systems to ensure financial sustainability and reducing overheads and personnel costs.
WSU spokeswoman Angela Church said there had not been a one-on-one communication between the university and department about the review of funding.
However, she said she was aware this was meant for historically disadvantaged institutions.
"It has long been our view that we are in one of the poor regions in the country and we have a compelling case for special funding because our students are from the poor backgrounds."
Former WSU administrator Professor Lourens van Staden had compiled a report about the institution's financial situation, which highlighted funding shortfalls for the university.
Church said the university was already reporting on its finances twice yearly to the department as required.
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