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.
The Jerusalem police commander subsequently ordered the Mount closed to allow for searches to be carried out.
The incident heightened tensions at the site, which is revered by Jews as the Temple Mount and by Muslims as the Noble Sanctuary.
The clashes come after weeks of tension over Bab al-Rahmeh and Bab al-Tawbeh, two areas used by Muslims to pray inside Al-Aqsa compound.
Although Palestinians in East Jerusalem, a part of the internationally recognized Palestinian Territory that has been subject to Israeli military occupation since 1967, they are denied their citizenship rights and are instead classified only as "residents" whose permits can be revoked if they move away from the city for more than a few years. In a statement, he called on the worldwide community to intervene.
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.
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.
Israel and Jordan are believed to be holding discussions to resolve the issue.
Last week, members of the Israeli police entered the Bab al-Rahmeh prayer area with their boots on, an act considered by Palestinians as a desecration, leading to protests.
The area has experienced a series of tense stand-offs in recent weeks after Muslim worshippers reopened an area known as the Gate of Mercy, closed by Israel in 2003. While the Israelis agree, they insist it must first be closed without renovations taking place, as a statement of Israeli authority.
On Tuesday, an incendiary device set alight an Israeli police position near the Dome of the Rock shrine inside the compound.