Police fired tear gas to disperse protests by hundreds of Al-Azhar University students Sunday at the university's male section in Nasr City, acting Al-Azhar student union president Mohamed Atef told Ahram Online.
Students also broke through the university's new electronic gates.
Mohamed Atef also said that a protest started at the university's female section, on the second day of the academic year.
"Down with the appointment of the university's council," were among the students' chants at the male section, which also condemned the hiring of Falcon company security guards and the arrest of students, said Atef.
Two Ahzar students were arrested yesterday and another one today, from their homes, according to Atef.
The clashes happened as a result of overcrowding at the new electronic gates and the "humiliating security check," said Atef. "It was a moment of anger," he added.
"The student union does not approve or condemn [the breaking of the electronic gates]," said Atef, adding that it was a reaction to new security measures like the fences, cameras and electronic gates, and that "the wave of protests will not stop."
Azhar student Amr Mostafa said that security forces are present at the gate and that the situation is now calm.
Investigations are being carried out to identify the participants in the incidents in order to take the necessary legal recourse against them, said university president Abdel-Hay Azab, according to Al-Ahram's Arabic news website.
"Small groups of students tried to obstruct the harmony of the studies and were confronted," said Azab.
The last academic year witnessed clashes between Azhar students and security forces in protests mostly supporting ousted president Mohamed Morsi.
Several students were killed in the violence. Hundreds of others were arrested and are still behind bars for protesting.
A decision to ban groups affiliated with political parties at the university was taken in September.
The university also banned around 500 students from living at the dorms