At least 13 people died and 140 were injured in clashes between Muslims and Coptic Christians in Cairo on Tuesday.
Both Coptic Christians and Muslims were killed in the violence, which began during a protest by Copts against last week's burning of a church.
Egypt's Sunni authority has urged Muslims to help rebuild the church, calling its destruction un-Islamic.
The clashes come two months after a suicide bomber killed 23 people at a Coptic church in Alexandria.
In January, an Egyptian man was sentenced to death for shooting dead six Copts and a Muslim policeman in Naga Hamady, southern Egypt.
The violence erupted when Coptic protesters blocked a highway in the Egyptian capital, protesting against the burning of the church in the province of Helwan.
The rally angered Muslims who wanted to pass through. Witnesses said both sides threw stones, and the army fired into the air to disperse the crowds.
The Grand Imam of al-Azhar issued a statement on Tuesday condemning the attack on the church in Atfih, Helwan governorate, as "a distortion of Islam".
Sheikh Ahmad al-Tayyib called on Muslim residents of the town to help start rebuilding the church and to refrain from sectarian violence, Egypt's official news agency, Mena, reported.
Meanwhile, thousands of Coptic protesters continued their sit-in outside the state television building. They are calling for the rebuilding of the church, better protection for Christians, and a full investigation into last week's attack.
Copts - who make up about 10% of Egypt's population - have often complained of harassment and discrimination, and argue that attacks on them go unpunished or result in light sentences.
The government in the predominantly Muslim country denies discriminating against Copts.