The "Freedom and Citizenship" conference is hosted by Al-Azhar, one of the leading Sunni Muslim authorities based in Cairo.
It comes as Coptic Christians in Egypt's Sinai flee attacks by Islamic State group jihadists who are waging an insurgency in the peninsula.
"Exonerating religions from terrorism no longer suffices in the face of these barbaric challenges," Al-Azhar's head Sheikh Ahmed Tayeb said in a speech on the opening day, referring to regional conflicts.
Coptic Christian Pope Tawadros II called for "fighting extremist thought with enlightened thought."
He said: "Egypt and the region have suffered from extremist thought resulting from a mistaken understanding of religion that has led to terrorism."
The conference, including Muslim muftis and Christian clergy such as Lebanese Maronite Patriarch Bechara al-Rahi, is to issue a closing statement yesterday.
IS, which controls parts of Syria and Iraq, views Christians as enemies who should either be killed or subjugated.
Tayeb, who represents a more moderate and traditional form of Islam, argues that groups like IS have perverted the religion.
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