Brotherhood students at Ain Shams University held a march on Wednesday to protest the banning of demonstrations on campuses. They chanted slogans against the government and the police.
Security personnel stepped up their presence to avoid clashes that may disrupt examinations.
Egyptian universities have seen waves of demonstrations since the start of the academic year in September by supporters of deposed president Mohamed Morsy, resulting in deaths on some occasions.
The Abdeen Urgent Matters Court ruled on Monday that no protests should be allowed inside universities except with a permit from the university president.
Meanwhile, scuffles occurred between Brotherhood students at Cairo University and University security after the students stormed the Supreme Council of Universities, which prompted security personnel to fire water cannons at them.
The scuffles left two students and two security personnel injured.
The Supreme Council of Universities unanimously agreed to allow police to enter campuses in case of violence.
Edited translation from Al-Masry Al-Youm
