Students have to behave responsibly and expect consequences if they try to set up a police vehicle with people in it, said National Director of Public Prosecutions Shamila Batohi.
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 conviction dismissed and an eight-year sentence.
Cekeshe was convicted of public violence and malicious damage to property after he tried to set up a police van during the protests.
He is serving an eight-year sentence at 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 aviator.
READ | Justice minister aims to get presidential pardon for #FeesMustFall activist Kanya Cekeshe
During Tuesday's meeting, DA MP Glynnis Breytenbach asked Batohi what Lamola's announcement does to the morale of prosecutors who work hard on issues, just to avoid the stroke of a pen.
Batohi said she and Lamola work closely together.
"He is very, very committed to the NPA's independence and also to supporting the NPA with the necessary executive resources the NPA can give," Batohi said.
"This is not something the minister has mentioned before. But as far as prosecutors are concerned, we know that 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 offenses.
"It was only with the more serious ones that we proceeded with the prosecutions."
"I mean students have to behave responsibly. You can't 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."