Unrest at Jerusalem's Temple Mount (also known as Haram esh-Sharif and the Al Aqsa Compound) led Israeli police to shut off access on Tuesday after several weeks of tension at the location.
Firas Dibs, spokesman for the Waqf, the Jordanian-appointed Islamic body that administers the site, said police had cleared almost all worshippers from the compound.
Monday's incident comes a day after Public Security Minister Gilad Erdan vowed that there will be "no second mosque on the Temple Mount" and that "God willing" Jews will be able to pray there freely in the near future.
File of Israeli flags near the Dome of the Rock in the Al-Aqsa mosque compound on December 5, 2017.
"Israeli soldiers stormed the Al-Aqsa compound and assaulted religious figures", Firas al-Dibs, a spokesman for Jerusalem's Religious Endowments Authority, a Jordan-run agency tasked with overseeing the city's Muslim and Christian sites, said in a statement. In a statement, he called on the worldwide community to intervene.
Israeli forces have been accused of responding with excessive force in some instances.
The U.N. Mideast envoy, Nickolay Mladenov, urged both sides to "respect the status quo" at the holy esplanade and exercise restraint "to avoid inflaming an already tense situation".
The closure of the sacred compound also drew censure from Jordan, the custodian of Muslim holy sites in Jerusalem.
The Waqf has staged periodic prayer-protests inside since late February to call for unrestricted access to the shuttered building.
The area inside the Gate of Mercy was sealed off by Israeli authorities in 2003, and it has been kept closed to stop illegal construction work there by the Islamic Waqf, the organization that administer the Temple Mount.
In the weeks since, the Israeli authorities have banned scores of Palestinians - including religious officials - from entering the Al-Aqsa, which for Muslims represents the world's third holiest site.
His office said it has been in communication with a number of parties including Jordan, in an effort "to pressure the occupation's government to halt this unsafe escalation".
Earlier Tuesday, a Jerusalem-district court rejected the state's request to close the flashpoint to allow Israel and Jordan to exhaust negotiation efforts.