Police arrested two University of Witwatersrand (Wits) students on Tuesday morning, including student leader Busiswe Seabe.
The two were taken into custody for allegedly contravening a court order obtained by the institution against students. The interdict stops large gatherings and singing on the campus.
Stun grenades were fired by police to disperse students outside the Great Hall earlier on Tuesday.
"We've only taken in two students from this morning's illegal gathering," said police spokesperson Captain Kay Makhubela.
He told News24 police would stay on campus throughout the day to monitor the situation. Public order policing units from both JMPD and SAPS have been deployed to the institution's campuses.
"We have deployed members but if needs be will call on more," said Makhubela.
Fees Must Fall leader Seabe claimed she was arrested for just asking questions but Makhubela dismissed this as just an allegation, stating that she would have to prove this when she appears in court.
The varsity's main campus has since calmed down with students milling about while others make their way to classes.