Police used teargas to disperse student protesters at Ain Shams University on Sunday, Al-Ahram Arabic news website reported.
Dozens of students had gathered outside the dentistry faculty for a protest in support of ousted Islamist president Mohamed Morsi, organised by Students Against the Coup.
They chanted slogans against the police and the military.
Protesting students reportedly stormed the university's pharmacy and commerce faculties.
A protest at the religious studies faculty of Al-Azhar University was dispersed by police using teargas.
Dozens of students at Alexandria University's commerce faculty protested to demand the release of four detained students.
The detained students are accused of taking part in violence during earlier protests.
Since the beginning of the academic year in autumn 2013, there have been frequent clashes between pro-Morsi students and security forces at campuses in Cairo and other cities.
In February, the interim authorities issued a decree allowing security forces to enter campuses and granting university administrators the right to expel protesting students.