Al-Azhar's Grand Imam Ahmed El-Tayeb threatened on Monday to go into solitary retreat in response to the current political strife and bloodshed.
"I might be forced to enter into a retreat in my home until everyone takes responsibility for protecting the sanctity of blood and preventing the country from a civil war," El-Tayeb said in a statement broadcast by Egyptian state TV.
Fifty-one people were killed and at least 435 were injured as former president Mohamed Morsi's supporters – largely from the Muslim Brotherhood – clashed with the Armed Forces at the Republican Guard in the early hours of Monday.
The Egyptian army said one officer died and 42 soldiers were injured, including eight in critical condition.
Former president Morsi was deposed by Egypt's Armed Forces on Wednesday following nationwide protests calling for his ouster. Judge Adly Mansour, the head of the High Constitutional Court, was sworn in as the country's interim president on Thursday.
In his statement, El-Tayeb, who approved Wednesday of the roadmap for a political transition post-Morsi, put forward several demands to solve the current political strife.
"Al-Azhar calls on those in power to open an urgent investigation into the incident [at the Republican Guard] and to publish its results for the public so that the truth is revealed and calm is restored," he said.
In addition, El-Tayeb said that a time-frame for the transitional period must be announced and should not exceed six months. There should also be a clear plan outlining a "democratic transition" that guarantees the people's unity, he said.
The Grand Imam asked that all political prisoners be released "and returned safely to their homes."
Several members of the Muslim Brotherhood, in addition to Islamist Morsi supporters, have been arrested or detained since the president's ouster.
El-Tayeb also called for the formation of a national reconciliation committee that would include "all factions" to reach consensus.
Earlier on Monday, Al-Azhar, Egypt's 1000-year-old seat of Islamic learning, condemned the "painful incident" in front of the Republican Guard, which it says will portend a dark time of strife.