Police General Abdel-Fattah Osman, an interior ministry aide, says security forces enter Egyptian campuses only after repeated requests by university administrators, although the law allows them to enter without permission.
During an interview with Al-Hayat TV on Tuesday Osman accused protesting students of breaking the law and inciting violence.
Clashes between pro-Muslim Brotherhood students and police erupted on Tuesday after police fired teargas at protesters demonstrating outside of Cairo University in Giza. A number of students were arrested and several people were injured, including three policemen.
"Are Molotov cocktails and bladed weapons tools of protest?" Osman asked. "We seized tools of sabotage, thuggery and destruction from a number of students."
He added: "Freedom of expression is a right everyone is entitled to, but in a peaceful way. These students did not stick to peacefulness and stooped to thuggery."
Osman accused students affiliated to the Muslim Brotherhood of ousted President Mohamed Morsi of trying to hamper university studies. He said that reinstating university guards with limited authority--a subject of debate as of late--would reduce troubles.
In November, the interim government issued a law allowing security forces to enter campuses without permission from university officials.
Engineering students at Cairo University have been staging a sit-in to demand accountability for the death of Mohamed Reda, who had been studying in the same faculty. He was shot dead recently during clashes with the police. The engineering faculty has suspended work indefinitely.
Since the start of the academic year in September, pro-Morsi student protests have taken place at a number of campuses across Egypt. Al-Azhar University has witnessed clashes between security forces and students in recent weeks.
On Tuesday, clashes re-erupted between security forces and Al-Azhar University students outside the campus. The student union began a strike in protest of security forces entering the campus the previous day.