The decision announced by Sheik of al-Azhar Mohammed Sayyed Tantawi came days after he said the face veil, or niqab, "has nothing to do with Islam."
His comments and actions have sparked an outcry from Islamists who see them as an attack on their religion and some rights organizations who believe banning the niqab violates constitutional freedom.
The explosive issue of how much of a Muslim woman's body should be covered remains contested among Islamic scholars.
The majority of scholars say the face veil is not required but is merely a custom that dates back to tribal, nomadic societies living in the Arabian desert before Islam began.
While a vast majority of Egyptian women wear headscarves, few wear the niqab, which is common in Saudi Arabia where the more conservative form of Wahhabi Islam is practiced. The trend seems to be gaining ground in Egypt, leading to government attempts to ban the face veil from public institutions.
Tantawi, who was appointed by the Egyptian government, first attacked the niqab Sunday during a field visit to a middle school where he asked a student to remove her face veil, according to local media.