Security forces have stormed Al-Azhar University to break up a peaceful protest by female students calling for the release of their colleagues detained at earlier demonstrations.
Teargas was used to disperse the protesters, who were supporters of the outlawed Muslim Brotherhood.
Meanwhile, dozens of Islamists belonging to "Students Against the Coup" staged a march at Cairo University. They vowed to show the "student movement is alive" and denounced government "repression and the arrest of students."
Small on-campus protests on Sunday erupted into clashes between Islamist students and police. Forty students were arrested as a result at several universities.
Last year, Egyptian universities faced serious unrest as students – mostly supporters of former president Mohamed Morsi's – protested his ouster in July, 2013 in what they describe as a "coup."
The government anticipated unrest on campuses this academic year by employing a private security firm to guard 15 public universities nationwide.
All politically affiliated groups and events have been banned by university administrations.
Already this term police have stormed at least five campuses and arrested dozens of students.
Since the beginning of the new academic year on 11 October, over 180 students have been arrested, according to the Association for Freedom of Thought and Expression, an independent rights body.
Egypt passed a protest law in November 2013 that bans all but police-sanctioned demonstrations and has been used to jail hundreds of people.