The clashes broke out when students who support former president Mohammed Morsi refused to allow other students on campus to take exams.
Media advisor to the Ministry of Health, Ahmed Kamal, said the clashes had left one person dead and four injured, Al-Ahram online reported.
Pro-Muslim Brotherhood students raided and set fire to buildings of the commerce and agriculture faculties and police fired teargas to disperse the mob.
The Interior Ministry said the protesting students had molotov cocktails and fireworks. Around 60 students were arrested.
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The Brotherhood, who activities were completely banned in September, was declared a terrorist group on Wednesday after the suicide bombing of police headquarters in Nile Delta.
The government said the movement was behind the attack - a charge it strongly denied.
This is the latest measure against the group, which is being targeted by the military-backed interim government. Thousands of Brotherhood members, including its top leaders, have been arrested and many put on trial.
Three people died yesterday as police fought Brotherhood supporters in Cairo, southern Minya and the Nile Delta.