Soldiers on Monday violated the status quo on the esplanade of the mosques in east Jerusalem by raising Israel's flag, the head of the Islamic Waqf organisation that oversees the compound charged.
"More than 180 soldiers from a special Israeli army unit today raised a large Israeli flag opposite the mosque of the Rock, which is a grave provocation," Sheikh Azzam al-Khatib told AFP.
The sprawling esplanade containing the Al-Aqsa mosque and the adjacent Dome of the Rock in the historic Old City is the third-holiest site in Islam after Saudi Arabia's Mecca and Medina.
It is also the holiest site for Jews, who refer to it as the Temple Mount because it was the location of the Second Temple, destroyed by the Romans in 70 AD.
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Sheikh Khatib said the soldiers entered the esplanade during a visit approved and organised by Israeli police.
He said he had made a complaint both to the Israeli police and to the Jordanian authorities. Jordan, which has a 1994 peace treaty with Israel, is the custodian of Muslim holy sites in Jerusalem.
Police spokeswoman Luba Samri confirmed to AFP that there had been an incident but said it concerned "a small flag," and said that a senior officer at the scene quickly intervened to expel the soldiers from the compound.
She said they would later face disciplinary measures.
Israel occupied the eastern sector of Jerusalem during the 1967 Six-Day War in a move never recognised by the international community, and later annexed it.
For Israelis, Jerusalem is their "eternal and undivided capital," but Palestinians claim east Jerusalem as the capital of their promised state.