Staff at the Cape Peninsula University of Technology's (CPUT) Bellville campus rushed to move their cars when somebody started stoning the vehicles on Tuesday.
"Staff are visibly shaken, they are traumatised," said a lecturer whose car had a brick thrown at it.
"This whole thing has been an emotional rollercoaster from the days of fees must fall," he said, speaking on condition of anonymity.
He said that several cars were hit, and staff members rushed to get their cars off the premises.
Spokesperson Lauren Kansley said there were sporadic incidents of protest action at the campus.
"We understand this to be linked to residence and campus catering issues," she said.
Kansley said CPUT had a surplus of residence beds so she did not believe it to be a true reflection of the real motivation behind the protests.
With regards to issues around campus catering, a re-modelling of the entire food offering service across the campus was underway.
Students were currently being catered for by food trucks.
She said a management committee would meet with student leaders weekly, and more regularly if needed, to avoid student concerns escalating.
The institution, however, remained open and operational.