Dozens of students were injured in the vicinity of the Defense Ministry as security forces dispersed them with tear gas.
Armored vehicles chased students and fired tear gas at them, while students responded with fireworks and rocks.
Hundreds of pro-Muslim Brotherhood students staged a march on Tuesday from Ain Shams University to the nearby headquarters of the Defense Ministry, blocking al-Khalifa al-Ma'moun Street.
Quarrels took place between protesters and frustrated drivers, while security forces intensified their presence at the Defense Ministry.
Meanwhile, hundreds of pro-MB students staged marches in Mansoura University and set fire to Israeli and UAE flags. They chanted, "We want a complete revolution," "Down with military rule," and "The police are thugs."
Dozens of Mansoura University faculty members staged a protest to demand the release of their detained colleagues. A security source said seven students were arrested in Assiut University during clashes with the security forces and three security personnel were injured.
A Health Ministry source in Assiut said 48 school students suffered from suffocation as security forces dispersed protests with tear gas. The students were transferred to hospitals, the source added.
In related news, protesting students at Al-Azhar University set a car on fire outside the Faculty of Agriculture and lit fireworks. Security forces headed to campus to control the protests and the fire.
Protests by supporters of toppled President Mohamed Morsy have swept through Egyptian universities since his ouster. Many students have been killed over the past months in clashes between the security forces and students.