Walter Sisulu University students accumulated R800m in debt during the Fees Must Fall protests, which has led to further protests at its campuses, the institution's spokesperson Yonela Tukwayo said on Monday.
The university closed some of its campuses indefinitely after violent students protests last week. Its campuses at Butterworth, Buffalo City and Mthatha remain closed.
Students are protesting over the quality and number of residences available to them, she said.
Speaking to News24 on Monday, Tukwayo said the university has battled to keep up with the maintenance of its residences as a result of poor fee payments by students.
"The reality is that students have not been paying their fees. We saw a big rise in non-payments during the fee protests. They have been putting off paying their fees in the hopes that the state would adopt a free fee education policy. This resulted in the debt accumulating and we ended up with R800m in December," she said.
In December 2017, President Jacob Zuma announced that government would subsidise free higher education for poor and working-class students.
This meant that South African households with a combined annual income of up to R350 000 would receive free education for the 2018 academic year.
The university, with the help of a grant from the Department of Higher Education, was in the process of building two new residences at its Butterworth and Mthatha campuses, which have been greatly affected by the protests.
However, Tukwayo said that the problems centred around the upkeep of already existing residences would continue because the "upkeep needs to come from the operations budget which comes from students fees".