Ten suspects were arrested and an investigation into the incident was ongoing, police said.
"Dozens of 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.
Police said that officers acted responsibly to deal with security threats, and that they needed to close the Mount to secure the area.
Palestinian President Mahmoud Abbas denounced the "dangerous Israeli escalation" and warned of "serious repercussions".More news: Papal advisor George Pell sentenced to 6 years in prison
Israeli border police secure one of the entrances of the Temple Mount compound in the Old City of Jerusalem after closing the access to the site on March 12, 2019.
Saif said incidents in Jerusalem was as a result of the silence of the worldwide community before the violation of all global agreements and human rights.
According to Israeli media outlets, Netanyahu's remarks were made during a ceremony to sign an agreement with the Israeli municipality of Jerusalem to build 23,000 housing units in the city within the coming five years.
The Temple Mount/Haram al-Sharif was re-opened to worshipers on Wednesday morning after a bout of fresh clashes at the contentious holy site the day before, amid soaring tensions over the status of a contested prayer area that has been closed off by Israel for more than a decade.
Violent altercations have erupted on several occasions over past weeks as thousands of worshipers have forced their way in to the contested area for Friday prayers.More news: Three-story building in Nigeria collapses with schoolchildren inside
Israel and Jordan are believed to be holding discussions to resolve the issue.
There were also unverified reports of Israeli police entering the Dome of the Rock.
Jordan has offered that the site be closed for long-term renovations. This disagreement has reportedly stood in the way of a deal. The gate had been closed by Israel in 2003 because it said that a Hamas-linked organization had taken control of the site and was acting against the interests of the Jewish State.
The groups said escalating tensions in Al-Aqsa Mosque is a continuation of arbitrary policies of Israel against Palestinians, land and sacred places, referring to raids in East Jerusalem's flashpoint Al-Aqsa Mosque complex.More news: Lonzo Ball becomes second Laker to be shut down for season