The unrest came on the final Friday in the Muslim holy month of Ramadan. Most of those injured suffered “upper-body injuries” the Red Crescent said, adding that 22 people had been taken to hospital.
Israeli police claimed forces entered the compound after “rioters” hurled stones and fireworks, including down towards the Western Wall, the sacred Jewish site below Al-Aqsa.
Witnesses stated police fired tear gas and rubber bullets.
Police said three people had been arrested, two for throwing stones and one for “inciting the mob”.
“For the past hour, the site has been quiet and [Muslim] worshippers are safely entering [the compound],” police added.
But tensions remain high at the site in the heart of Jerusalem’s old, walled city, part of Israeli-occupied East Jerusalem.
Over the past two weeks, nearly 300 Palestinians have been injured in Israeli incursions at the Al-Aqsa compound, Islam’s third-holiest site.
Muslim leaders have been angered by a recent uptick in the number of Israeli settlers entering the Al-Aqsa Mosque compound.
The longstanding convention has been that only Muslims are allowed to pray at the compound, but, according to the Jerusalem Islamic Waqf, nearly 3,700 Israeli settlers have entered the Al-Aqsa Mosque compound over the past week to mark the Jewish festival of Passover.
Most Orthodox Jews do not pray inside the compound, believing it to not be religiously acceptable, and Jerusalem’s Chief Rabbinate also forbids prayer there.
However, a growing number of Israeli religious nationalists have encouraged Jewish prayer on the site, with elements calling for the construction of a Jewish temple there.
The growing presence of the movement has led to many Palestinians fearing that Israel is seeking to divide the compound and create a space where Jews may worship.
In an apparent attempt to ease tensions, Israel’s foreign minister Yair Lapid has stressed that the government was committed to the status quo at the compound, and said that no plan to divide it exists.
However, Palestinians living in the occupied West Bank still face tough restrictions on visiting the Al-Aqsa compound, a national symbol for Palestinians, with travel being almost totally restricted for most of the year, and only allowed for certain age groups during Ramadan. In effect, this means that many Palestinians who live only miles away from East Jerusalem have never been able to visit.
Israel says that the measures are necessary for security reasons. The fresh unrest comes on the last Friday of Ramadan, with the end of the Muslim holy month coming early next week.
Violence in Israeli-occupied East Jerusalem has raised fears of another armed conflict similar to an 11-day Israeli assault on Gaza last year which was triggered by similar unrest at the mosque.
Recent weeks have seen isolated rocket fire from Gaza towards Israel and Israeli reprisals, but no casualties reported on either side. The Al-Aqsa tensions have come against a backdrop of violence since March 22 in Israel and the occupied West Bank and Gaza.
At least 26 Palestinians and three Palestinian citizens of Israel have died during the period, most of them in raids by Israeli security forces in the occupied West Bank.
Twelve Israelis and two Ukrainians were also killed in four separate attacks inside Israel. Two of the deadly attacks were carried out in the Tel Aviv area by Palestinians.