Palestinians and Israeli police clashed in Jerusalem's Al-Aqsa mosque on Friday, killing 42 people after weeks of violence at the flashpoint site, the Palestinian Red Crescent said.
The unrest came on the final Friday in the Muslim holy month of Ramadan. The Red Crescent said 22 people had been taken to hospital, and none of the injuries were serious.
Israel's police said that troops entered the compound after rioters hurled stones and fireworks, including down the Western Wall, the sacred Jewish site below Al-Aqsa.
The statement said officers used riot dispersal means to contain the unrest. Witnesses and AFP reporters said police fired tear gas and rubber bullets.
Three people were arrested, two were charged with throwing stones and one for inciting the mob for the past hour and Muslim worshippers are safe entering the compound police said.
But tensions remain high at the site, located in the heart of Jerusalem's old, walled city, part of Israeli-annexed east Jerusalem.
Over the past two weeks, nearly 300 Palestinians have been injured in clashes at the Al-Aqsa compound, Islam's third-holiest site, which is the most holy site for Jews who call it the Temple Mount.
Israel's incursions into the site during Ramadan have raised global concern, but the Jewish state has insisted it was compelled to act against operatives from the Islamist groups Hamas and Islamic Jihad, who were trying to spark widespread unrest across Jerusalem.
Israel's Foreign Minister Yair Lapid stressed that the government was committed to the status quo at the compound, meaning an adherence to the long-standing convention that only Muslims are allowed to pray there.
Jews are allowed to visit the Temple Mount.
Some Muslim leaders have been angered by a recent increase in such visits, fearing that Israel was trying to divide the compound and create a space where Jews may worship. Lapid told reporters that no such plan exists.
Violence in Israeli-annexed east Jerusalem has raised fears of another armed conflict similar to the 11 day war between Israel and the militant group Hamas last year, triggered by similar unrest at Al-Aqsa.
There have been isolated rocket fire from Gaza towards Israel and Israeli reprisals over the past few weeks, but there has been no casualties reported on either side.
The violence in Israel and the occupied West Bank has resulted in the Al - Aqsa tensions since March 22. Twelve Israelis, including an Arab-Israeli police officer, and two Ukrainians, were killed in four separate attacks inside Israel. Two of the deadly attacks were carried out by Palestinians in the Tel Aviv area.
A total of 26 Palestinians and three Israeli Arabs have died during the same period, among them perpetrators of attacks and those killed by Israeli security forces in West Bank operations.