"Jerusalem is a red line," its chief Ahmed Abul Gheit said in a statement, adding that "no Arab or Muslim will accept violations" against the city's holy sites.
Deadly clashes have rocked Jerusalem since Israeli authorities installed metal detectors at entrances to the Haram al-Sharif compound, known to Jews as the Temple Mount, following a mid-June attack that killed two policemen.
Palestinians view the measure as an Israeli attempt to assert further control over the site, the third most holy place in Islam and the most revered site in Judaism.
Abul Gheit accused Israel's government of "adventurism" and said its moves could trigger a "crisis with the Arab and Muslim world".
The compound, which includes the revered Al-Aqsa mosque and the Dome of the Rock, has been the focal point of tensions between Israelis and Palestinians for decades.