Last year's #FeesMustFall student protests cost universities R150 million in damages, Higher Education Minister Blade Nzimande said on Wednesday.
"Our preliminary report suggests that an estimated R150 million of damage to public property was caused last year during the #FeesMustFall protest. Fortunately this only affects some institutions," he said.
In addition, the cost of providing extra security at several universities this year to prevent more protests was proving exorbitant.
On Monday, University of Johannesburg Vice Chancellor Ihron Rensburg told journalists that universities were spending a little under R2 million on extra security every month.
Nzimande called on students and staff who still had demands and wanted to continue protesting to do so peacefully.
"This will negate the need for security in our campuses. Violence is unacceptable," he said.
Nzimande met 26 representatives of higher learning institutions to discuss preparations and arrangements for the new academic year on Wednesday. Also in attendance were senior National Student Financial Aid Scheme officials.
Those in attendance held a frank discussion and expressed appreciation for the support that government and the ministry had given them during the student protests.
He said the meeting confirmed that all qualifying students who had been offered a place at a university and who qualified for NSFAS could register without upfront payment.
Each institution had payment plans in place for all qualifying students, he said.
Several universities suspended registration after disruptions by students last week. They wanted free registration for all students.
#FeesMustFall is a student-led protest movement that began in mid-October 2015 in response to a proposed increase in fees at South African universities.
Protests started at Wits University and spread to the University of Cape Town and Rhodes University, and then to other institutions across the country.
President Jacob Zuma eventually announced there would be no fee increases in 2016.