The violent protests have led to damage to property and interference in the academic programmes in some institutions, Minister of Higher Education and Training Blade Nzimande said.
According to police, dozens of people suspected of involvement in acts of violence have been arrested, Xinhua news agency reported.
Such protests "are wholly unacceptable and provide no solution to student concerns," Nzimande said in a statement.
Students have threatened to disrupt all universities if their demand for no increase is not met.
Protests erupted on Monday after Nzimande announced that universities can raise tuition fees for 2017, provided the hike will not exceed eight per cent.
During the protest in Wits University in Johannesburg, the police fired stun grenades and rubber bullets at protesters in an attempt to disperse them.
"It is most disturbing to see such violent protests enflamed by rogue elements after wide consultation was undertaken on the measures announced this week to address the ongoing issue of university fees," Nzimande said.
The government has heeded the call of students by subsiding fee increase in 2017 to poor, working class and "missing middle" students, the minister said.
"We cannot subsidise all students in the same manner. Those from households with an income of below $42,000 per annum have been assisted by the gap funding from government as announced this week," he said.
Those with the means to do so should contribute to increasing university costs by paying fees, said the minister.
Fees remain a significant income stream for universities, together with the government subsidies and third stream income, according to Nzimande.
"The dialogue with students must continue. However, damage to property and violence can never be tolerated," said Nzimande.
He reiterated that his door is always open for any further engagement and discussion but such engagements cannot take place in an environment of violence and destruction.
The minister called on law enforcement agencies to act immediately, within the boundaries of their mandate, against any hooliganism resulting in violence and destruction.
He also called on university vice chancellors to tighten up security and take any measures necessary to prevent any form of violence and destruction of property.
South African universities were hit by widespread protests over fee increases last year too. According to official figures, the unrest cost more than about $10.8 million in damages.
The government then suspended fee increases for 2016 and provided universities with billions of rand for the shortfall.
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