The government, grappling with a budget deficit equivalent to nearly 4 percent of economic output, says education subsidies should not be paid for at the expense of other sectors of the economy such as health and housing.

It has also said 2017 university fees may rise by up to 8 percent.

Police clashed sporadically with student protesters on Tuesday at the University of the Witwatersand (Wits), Talk Radio 702 said. Wits was hit by violence on Monday after reopening following angry protests that forced its closure last week.

The team set up by Zuma consists of eight ministers including Higher Education minister Blade Nzimande and Minister of Police Nathi Nhleko, and is tasked with resolving the crisis.

The main opposition Democratic Alliance party criticised Zuma, however, for excluding Finance Minister Pravin Gordhan.

"At the heart of the crisis is the chronic under-funding of higher education over the last decade," it said in a statement.

Zuma's government has said it will continue subsidising university costs for the poorest students but could not afford free education for all.

"We are not saying... everybody must receive free education, even if the parents can afford, because we have got to balance the resources," Zuma told a news conference in Nairobi on Tuesday during a state visit to Kenya.

The Wits Student Representative Council said in a statement that they would be continuing the struggle for free education.

Some students are demanding all universities be shut down until the government provides free education.