One protester was shot dead as students fought police at Al Azhar University, health ministry officials said. Students denied starting blazes in the business faculty, where exams had to be postponed, and the agriculture faculty.
Authorities have cracked down on the Brotherhood since July, when Islamist President Mohammed Morsi, who belongs to the group, was deposed by the army.
The Brotherhood, which had been banned since September from all activity, was declared a terrorist group on Wednesday following a suicide bombing of a police headquarters in Nile Delta.
The government said the movement was behind the attack – a charge it strongly denied.
It is the latest measure taken against the group, which is being targeted by the military-backed interim government. Thousands of Brotherhood members, including its leadership, have been arrested and many put on trial.
Members were rounded up on Thursday after a bomb hit a bus in Cairo, injuring five people.
Three people died on Friday as police fought Brotherhood supporters in Cairo, southern Minya and the Nile Delta.
US Secretary of State John Kerry called his Egyptian counterpart to “express concern” about the recent waves of arrests and called for an “inclusive political process”, state department spokeswoman Jen Psaki said.
Al Azhar, one of the main centres of Sunni Muslim learning, has been the scene of repeated clashes between Islamist students and police in recent months.
Mr Morsi’s government – the first to be democratically elected in Egypt – was toppled on 3 July following widespread anti-Brotherhood demonstrations.
The ousted president was arrested and faces several criminal charges relating to his time in office.
His trial opened in November – with the former president saying he was still Egypt’s legitimate leader and refusing to wear the uniform required for court – but was then adjourned until 8 January while lawyers examine documents.
Earlier this week, Egyptian police arrested Hisham Qandil, who became Egypt’s youngest prime minister since 1954 in August 2012.
He was caught in a mountainous area with smugglers trying to flee to Sudan, officials said.
Mr Qandil was sentenced to a year in prison while in office for not carrying out a court ruling to renationalise a company that was privatised in 1996.
Although not a member of the Brotherhood or any other Islamist political organisation, he represented an alliance of pro-Morsi Islamist groups in meetings with European Union mediators, who tried to persuade the military-installed interim government to launch a fully inclusive transition process that included the Muslim Brotherhood.
The 85-year-old Islamist movement was banned by Egypt’s military rulers in 1954, but registered an NGO called the Muslim Brotherhood Association in March this year in response to a court case bought by opponents who contested its legal status.
The Brotherhood also has a political wing, the Freedom and Justice Party (FJP), which was set up in 2011 as a “non-theocratic” group after the uprising that forced President Hosni Mubarak from power.
Following Mr Morsi’s overthrow and the suspension of the Islamist-friendly 2012 constitution, the Cairo administrative court and the social solidarity ministry were tasked with reviewing the Brotherhood’s legal status.
In September, a ruling by the Cairo Court for Urgent Matters banned the Brotherhood itself, the NGO, as well as “any institution derived from or belonging to the Brotherhood” or “receiving financial support from it”.
BBC News
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