Protests have spread from Johannesburg’s Wits University, closed last week after thousands demonstrated on campus, to the universities of Rhodes and Cape Town (UCT).
Wits University agreed to suspend a 10.5% tuition fee increase on Friday, pending negotiations with students.
Protesters argue that poorer, mainly black students would be worst affected.
A statement from Wits University said that a decline in state subsidy over the years, combined with inflationary pressures, were behind the fee increases in recent years.
Higher Education Minister Blade Nzimande, appearing on national broadcaster SABC, said that he was convening a meeting on Tuesday for university administrators, employees and student leaders to discuss fee increases.
The minister urged university authorities “to exercise greater caution and sensitivity in the process of determining fee increases”, saying a solution would need to balance the difficulties of poorer students with the financial pressures currently facing the system.
The hashtag #FeesMustFall has been trending across South Africa, in an echo of #RhodesMustFall, which was used by UCT students in their successful campaign to have a statue of British colonialist Cecil Rhodes removed in April.
At Rhodes university in Eastern Cape Province, classes were suspended after students armed with sticks set up barricades of burning tyres, blocking road access to main campus entrances.
UCT is “notoriously the most expensive university in the country, if not on the continent,” Rori Moseli, a second year student at UCT and a member of the student representative council, told the BBC’s Focus on Africa radio programme.
He said that students were seeing fee increases of 10-12% every year, roughly twice the rate of annual inflation in South Africa.
“For a long time, we’ve bought up these issues… but it seems as though we get ignored,” he added.
Students at UTC broke into a building on campus on Monday, after being locked out and ordered to leave the campus by university authorities.
UTC has secured an order from the High Court in Cape Town to “prevent protesters from interfering with university operations”, which comes into force at 07:00 local time (05:00 GMT) on Tuesday.
The order authorises the police to enforce its terms, which include a ban on barricading entrances and occupying buildings on the university campus.