Thousands gathered in Luxor and Cairo on Friday in support of Al-Azhar Grand Imam Ahmed El-Tayeb.
The protesters claimed El-Tayeb is being targeted by the Muslim Brotherhood because it wants to control Al-Azhar.
After an outbreak of food poisoning at Al-Azhar University hospitalised more than 500 students on Monday, there were calls by some for the grand imam to be removed.
Protesters on Friday carried signs reading "Al-Azhar is a red line," and chanted against the supreme guide of the Muslim Brotherhood.
The head of the dormitory where the incident took place has been arrested and the university president has been sacked.
Dozens also showed support for the grand imam in Alexandria and Mansoura on Friday afternoon.
Ahmed El-Tayeb is a native of Luxor.