Pretoria - The Economic Freedom Fighters Student Command shut down proceedings at the University of South Africa's Sunnyside campus on Friday morning.
Students from the ANC Youth league clashed with EFF students claiming that their shutdown was uncalled for.
Workers of the university were told to stop working and close the doors.
Scores of police officers roamed around the streets to maintain the situation as traffic was backed up.
The EEFSC claimed that the university has not been assisting students with registration and turned more than 500 students away since Wednesday.
EFFSC said Unisa's online system lost documents that were attached and as a result students could not register.
The EFFSC accused Unisa of not taking it's students serious.
ANC Youth League students said they did not support the EFFSC's use of force to make their demands heard.
EFFSC leadership said it was going to shutdown the institution again on Monday and it planned to triple the number of protesters.
Wadzanai Mazhetese of the EFFSC and also member of the National Student Representative Council accused Unisa of planning to stop funding students who enrolled for higher certificate courses from its Nsfas fiscus.
Jackson Ledwaba of Sasco and the ANCYL said the EFFSC was lying in it's claim that Unisa's Nsfas fiscus would no longer be used to fund higher education students.
He said Sasco had agreed to give Unisa this week to settle all its queries for things to run smoothly from the next week.
He said: "The EFF need to understand that although the president pronounced on free higher education for the poor, it needed to be ushered it peacefully. The EFFSC's demands did not warrant a protest or university shutdown."