Students at Al-Azhar University hurled rocks at the police and tried to block traffic on a major thoroughfare outside the campus in eastern Cairo, a security official said. The official spoke on condition of anonymity because he was not authorized to speak to reporters.
Student Spokesman Mahmoud Salah said the police later left the area, and protesters who had taken cover inside the dorm went out to continue their protest.
Salah said the students had lit a fire at the dorm gates to lessen the impact of tear gas fired by the police. He also said a number of students were injured and claimed the police fired shotgun pellets.
The security agencies always deny using them.
With the start of the school year in September, Egypt's universities have become the main venue for protests by supporters of Islamist President Mohammed Morsi, ousted in a popularly backed military coup in July.
The Muslim Brotherhood, Egypt's largest Islamist group and the one from which Morsi hails, has organized protests, with marches on campuses nearly every day. Many of them have led to clashes with security forces.
But Al-Azhar University, with largely Islamist students, has seen persistent protests against Egypt's military-backed government.
Last month, 12 students from the same university were sentenced to 17 years and fined for participating in protests and clashes on the campus. Another 21 students from Al-Azhar were on Sunday referred to trial.
Salah said Sunday's protests were fuelled by the new referral, as well as a crackdown earlier in the day by university security against female protesters.
Students also protested Sunday at a university in the Nile Delta city of Mansoura, and at Cairo University.
In Mansoura, the students set a police car on fire, another security official said. He too was speaking on condition of anonymity.
Authorities have cracked down on Morsi supporters since last summer's coup, widening a net of arrests and legal prosecution to include senior leaders as well as students and protesters.
The crackdown has recently broadened to include other non-Islamist critics of the current authorities, and a new protest law was passed last month that tightly restricts public gatherings and increases penalties for violators.
The trial of three prominent non-Islamist activists referred to court in accordance with the new law on charges of taking part in an illegal protest and assaulting policemen began Sunday.
Ahmed Douma, Ahmed Maher and Mohammed Adel were some of the most prominent figures of the 2011 uprising against longtime autocrat Hosni Mubarak. Their referral is the first of activists according to the new protest law.
Defense lawyer Amr Imam said judges booked the case for a verdict on Dec. 22.
Besides asking for the defendants' release, the lawyers also said the protest law is unconstitutional for violating the right to free assembly. They asked the court to seek the opinion of the country's constitutional court, Imam said.
Khaled Dawoud, member of the liberal al-Dustour party, said the trial bodes ill for freedom of expression.
"I think that today's trial aims at sending a clear message to all activists that the freedoms that the Egyptians have enjoyed after the ouster of Mubarak are no longer allowed," he said. "It's a very negative message that the government is sending to all the activists who fought for freedom" since the 2011 uprising.
Also on Sunday, security officials said the bureau chief of al-Ahram newspaper in the southern city of Assuit was arrested following a complaint by local police.
Prosecutors are investigating accusations that Hamada Said "misreported" on a protest in Assuit late last month, by among other things inflating the number of protesters who took part in a pro-Morsi rally and by claiming the police was protecting the rally, held in violation of the new protest law.
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