Students have to behave responsibly and expect consequences if they try to set alight a police vehicle with people in it, National Director of Public Prosecutions Shamila Batohi said.
She addressed the Portfolio Committee on Justice and Correctional Services on Tuesday.
A day before, the #FeesMustFall activist Kanya Cekeshe failed in his bid to have his his conviction and eight-year sentence dismissed.
Cekeshe was convicted of public violence and malicious damage to property after he tried to set a police van alight during the protests.
He is serving an eight-year sentence in Leeuwkop Correctional Services in Bryanston.
Shortly after Monday's verdict, Justice Minister Ronald Lamola tweeted that his department is in the process of urgently assisting Cekeshe with an application for a presidential pardon or other legally available avenues.
During Tuesday's meeting, DA MP Glynnis Breytenbach asked Batohi what Lamola's announcement does to the morale of prosecutors who work hard on difficult matters, only for it to be undone with the stroke of a pen.
Batohi said she and Lamola work closely together.
"He is very, very committed to the independence of the NPA and also to supporting the NPA with the necessary resources the executive can give to the NPA," Batohi said.
"This is not something that the minister hasn't mentioned previously. But as far as the prosecutors are concerned, we know that notwithstanding in some instances what the executive might do, we need to do what we have to do."
She said many students were arrested, but the NPA decided to withdraw many of the less serious offences.
"It was only with the more serious ones that we proceeded with prosecutions."
"I mean, students have to behave responsibly. You cannot burn libraries, or try to burn a police car with people in it. These are serious cases, this will have to be looked at," Batohi said.
"But as far as prosecutors are concerned, we will continue to do what we have to do."