Nearly a dozen protesters from both sides were injured in the melee at Zagazig University.
The chairman of the school was considering canceling classes for the week, al-Masry al-Youm said.
The protest was one of several held by Muslim Brotherhood supporters on campuses around Egypt. The demonstrators were protesting what it called the police state instituted by the military-backed government that earlier this year deposed President Mohamed Morsi.
The government was on the offensive Sunday in a village north of Minya, an area considered a stronghold of Islamist militants. Police raided the village of Bani Warkan and arrested 13 suspects after a shootout.
Security sources told al-Masry al Youm those arrested were suspected of carrying out arson attacks on public buildings in the area. They were also allegedly in possession of weapons stolen from a police station last month.