Police have arrested 144 protesters over violent clashes at a university in Cairo that left five students injured, one critically, Egypt's ministry of interior has said.

The ministry said that the critically injured student was in intensive care with a bullet wound to the chest after the clashes at Al-Azhar University on Monday.

Riot police fired tear gas at protesters at Al-Azhar University and a security official said several police cars were set on fire and petrol bombs thrown at officers in fresh clashes.

The students, supporters of ousted former president Mohamed Morsi, have held persistent protests since the start of the academic year in September.

The clashes came as Mohamed Badie, the leader of the Muslim Brotherhood, appeared in court for the first time since he was arrested in a state crackdown on the group following the army overthrow of Morsi.

Mahmoud Subeiha, the head of university security, told Egypt's private CBC TV that he asked the police to enter the campus Monday to put down the protests, which have frequently descended into clashes with police.

The students had rallied on Sunday against the referral of 21 of their colleagues to trial for earlier protests.

Meanwhile, Brotherhood General Guide Badie, 70, denied his group had perpetrated any violence, speaking from the cage reserved for defendants where he appeared with other prominent Islamists, including Mohamed el-Beltagi and Essam el-Erian.

Badie murder probe call

"Why aren't you investigating the murder of my son, and the burning of my house and the groups' offices?" said Badie, referring to his 38-year old son killed in August 17 protests ignited by the violent dispersal of Brotherhood

sit-ins.

The case being heard on Monday relates to violence that flared in mid-July near a Brotherhood protest camp at Cairo University. Badie faces charges including inciting the violence.

Morsi's downfall triggered the worst bout of internal strife in Egypt's modern history.

The security forces killed hundreds of Morsi's supporters during protests and some 200 soldiers and policemen have been killed. The army deposed Morsi on July 3 following mass protests against his rule.

Most of the Brotherhood's leadership has been arrested since then.

Morsi is himself standing trial on charges of inciting the killing of protesters during violence outside the presidential palace a year ago. His trial began on November 4.

The defendants interrupted Monday's session with chanting against generals whom the Brotherhood says have stolen power from the country's first freely elected head of state.

"Down with military rule," shouted Beltagi, leading the other defendants in chants.

The men on trial in the case include Bassem Ouda, the former minister of supplies.