A group of students set fire to the University of Fort Hare (UFH) indoor sports centre on Sunday night, a few hours before the start of mid-year exams.
The fire was started in the foyer of the centre at the university's Alice campus.
Furniture was also torched, a university shop was vandalised and windows of a computer lab were smashed, UFH spokesperson JP Roodt said.
"We condemn rumours on social media that the UFH indoor sports centre was completely gutted and destroyed by fire. Only the foyer area was affected," Roodt added.
The university has launched an investigation into the "unlawful" gathering but was "perplexed over the trigger of the event", it said on Monday morning.
"Allegations circulating on social media of congested exam timetables as the basis for the violence on campuses are unfounded for several reasons," said Roodt.
"Students and faculties were consulted ahead of the exams; exam module clashes were brought to the attention of the examinations department by faculties and students, and adjustments were made; and no formal complaint over the exams timetable clashes, as a student affairs concern affecting the majority of the student body, was brought to management by the SRC."
He added that "outlier cases of congested individual exam timetables" were not new and should not be the source of protest action.
"The university is busy obtaining eyewitness reports by students that witnessed the violence. We are also reviewing social media posts ahead of the event and we are examining CCTV footage to identify perpetrators.
"The university is certainly not ruling out foul play or the deliberate sponsorship of student violence," Roodt added. UFH management has resolved that exams will proceed as scheduled.
Only morning sessions on Monday at both the Alice and East London campuses have been rescheduled. "Starting from the afternoon session today, the rest of the university's exams will proceed as planned.
The university will also deploy security to ensure the safety of our students whose rights to education have been infringed," Roodt said.