President Abdel-Fattah El-Sisi has accused Al-Azhar's Grand Imam Ahmed El-Tayeb and other clerics of failing to develop Egypt's religious discourse.
"You are the one responsible for religious discourse, and God will ask me whether I am satisfied [with your performance] or not," El-Sisi said of El-Tayeb on Tuesday.
"The role of clerics is not to give speeches in mosques, but to spread peace among humanity," El-Sisi added.
"At last year's ceremony, when I tackled the idea of a religious revolution, I didn't mean imposing [change through] violent actions, rather I meant to revolutionise our thoughts in order to make them to fit the time and also to improve the image of Islam."
"The main problem is that we don't understand our religion ," he said. "And we cannot accept those people who misuse Islam to promote violence and extremism."
In January, El-Sisi said during the World Economic Forum held in Switzerland that Islamic tolerance was not clear to the world because of terrorism.
"We should stop and change our religious rhetoric from faulty ideas which lead to (terrorism)," El-Sisi said, adding that this could only be achieved by scholars from Al-Azhar, the highest institute of Sunni Islamic learning.
"This has nothing to do with creed. No one will touch the pillars of Islam," he said.
Al-Azhar has been criticised for failing to combat the growth of Islamic extremism and atheism in Egyptian society.
El-Sisi made the comments at the annual ceremony of Leilat Al- Qadr, which takes place during the last ten days of Ramadan.