Clashes broke out following Friday prayers between Al-Azhar students and security forces at the university's dormitories.
Ahmed Saeed spokesperson for Al-Azhar's protestors told Al-Ahram Arabic news website that at least five students were arrested as they were protesting the detention of their colleagues and chanting against the police and the army.
Meanwhile security forces were deployed to several areas in Greater Cairo in anticipation of any protests organised by loyalists of deposed president Mohamed Morsi.
Roads leading to the interior ministry in downtown Cairo and the Giza security directorate were blocked.
Security presence was also beefed up around Rabaa Al-Adawyia -the former main site of pro-Morsi demonstrators- and the vicinity of the Ittihadiya presidential palace.
Around tens of protesters gathered in Cairo's Ain Shams district to denounce the presidential candidacy of Abdel-Fattah El-Sisi ,seen by loyalists of the Islamist president as being the architect behind his ouster.
A similar demonstration took place in Giza's Mohandeseen with protesters holding pictures of Mohamed Morsi and chanting "Sisi will not rule", according to Al-Ahram.