The official Palestinian news agency Wafa said dozens of worshippers who were spending the night praying were injured in the police raid at dawn on Wednesday, drawing condemnation from the Palestinians and Arab nations.
At least 400 Palestinians were arrested on Wednesday who remain in Israeli custody, according to Palestinian officials.
The Israeli raid comes as Muslims mark the holy month of Ramadan and Jews prepare to begin the Passover festival on Wednesday evening, raising fears of a wider conflagration. A similar raid two years ago had triggered a wider conflict, with Israelis launching an 11-day assault on Gaza Strip.
The 35-acre mosque compound is referred to as al-Haram al-Sharif, or the Noble Sanctuary, by Muslims, and as the Temple Mount by Jews. The site has been the most contested piece of territory in the Holy Land since Israel occupied East Jerusalem, including the Old City, in 1967, along with the West Bank and Gaza Strip.
Israeli police said they moved in after “several law-breaking youths and masked agitators” brought fireworks, sticks and stones and barricaded themselves into the mosque.
Police said they dispersed groups of youths with stun grenades and rubber bullets inside the mosque compound. One officer was injured in the leg, while some 350 people were arrested, they said.
Tensions have been steadily rising since Israeli Prime Minister Benjamin Netanyahu’s new far-right government took office late last year.
The police force is overseen by Itamar Ben-Gvir, an ultranationalist with a history of violent rhetoric and actions against Palestinians.
The Palestinian leadership condemned the attack on the worshippers. The spokesman of Palestinian President Mahmoud Abbas, Nabil Abu Rudeineh, warned Israel that such a move “exceeds all red lines and will lead to a large explosion”.
The government of Jordan, which serves as the custodian of the mosque, condemned the Israeli raid “in the strongest terms”. The foreign ministry warned “of the consequences of this dangerous escalation and held Israel responsible for the safety of the blessed Al-Aqsa Mosque”.
Israeli-Palestinian violence has surged over the last year, as the Israeli military has carried out near-daily raids on Palestinian cities, towns and villages to quell Palestinian resistance against Israeli occupation.
More than 90 Palestinians have been killed by Israeli fire this year. Palestinian attacks against Israelis have killed 15 people in the same period.