A number of Azhar faculty members and students filed a legal complaint on Sunday, accusing pro-Muslim Brotherhood protesters of beating them and preventing them from entering campus.
The protesters had rallied at the Nasr City campus to demand "the return of legitimacy" and the release of arrested protesters.
The university banned 205 students from entering campus earlier due to their involvement in confrontations in November.
Professor Laila Shokr told Aswat Masriya that she was beaten badly and that one of the protesters pulled her headscarf from off of her head and her earring.
She added that her colleague, Professor Neveen Sayed Ahmed, was also beaten and bitten by the students for standing up for her.
When Shokr called the dean of the faculty, Souzan Gamal al-Din, she told her that she was also beaten while her eyeglasses were broken and headscarf was pulled off of her hair.
The protesters, who are not over 200 women, were gathered to make sure classes do not take place, Shokr said.
Azhar University has seen several confrontations recently with pro-Mohamed Mursi supporters staging demonstrations and disrupting classes on regular basis.