At the Bellville campus, two buses were set alight and windows at the administration building smashed overnight on Tuesday.
The incident came after students who were evicted from a conference room had erected makeshift structures. The structure made from cardboard, plastic and wood were to highlight the shortage of accommodation.
Police spokesperson FC van Wyk said cases of malicious damage to property and arson were registered.
“Police officers are still deployed in Athlone and Bellville to maintain law and order. We're urging protesters to carry themselves in an orderly manner that does not infringe on the rights of others.”
Twelve of the 21 protesting students arrested at the Athlone campus for public violence received R500 bail each at Athlone Magistrate's Court yesterday.
Van Wyk said the institution has an interdict against any protest action by the students. He said students were asked to disperse as the protest was not permitted and deemed illegal.
Public Order Police used rubber bullets and stun grenades to disperse hundreds of students who gathered outside the campus.
The students blocked the main entrance of the college with desks, blocked Klipfontein Road with large concrete rocks and stoned motorists. Parked government vehicles were overturned.
They demanded more securities at the college following a number of break-ins, shuttles, hours at the library to be extended and an assistant to help.
They also complained about water shortages, which they claimed posed health risks to them.
Athlone campus SRC chairperson Thobile Tshefu said: “Nine students were released on Tuesday night for ‘lack of evidence’. We don’t know if there was evidence against the 12 released today.
“We only want management to engage with us like it’s engaging with Bellville SRC because it claims it has answered all our grievances."
At District Six campus students who are also seeking accommodation, the majority of whom were not from the province, threw litter at the student centre.
CPUT management said attempts to shut down campuses, disrupt lectures and damage property will never be the answer to effective engagement.
“The positive start of the 2019 academic year has however been dealt a blow after the institution was the victim of arson and sabotage attacks overnight.
“This is demoralising for the dedicated staff who have already persevered through a traumatising crisis period since 2015.
“At least 21 people, believed to be CPUT students, were arrested in connection with public violence outside of the Athlone campus.
“These are now criminal matters and these individuals are risking their academic futures and the possibility of a criminal record may now shadow them long after they have parted ways with CPUT.
“The well-being of 400 00 staff and students will not be held to ransom by a minority pursuing a selfish agenda.
“Attempts to shut down campuses, disrupt lectures and damage property will never be the answer to effective engagement.
“At the moment teaching at only the Athlone campus is suspended, but it remains open and staff are reporting for duty.
“Clinical trials also continue, the rest of CPUT is open and operational,” management said.