Mosque authorities say Israeli police entered before dawn, after 7 Palestinians were killed since Wednesday.
Israeli police have raided the Al-Aqsa Mosque in occupied East Jerusalem, with medics saying at least 59 Palestinians have been injured in violence that followed.
The Islamic endowment that runs the site said Israeli police entered in force before dawn, as thousands of worshippers were gathered at the mosque for early morning prayers.
Videos circulating online showed Palestinians throwing rocks and police firing tear gas and stun grenades. Others showed worshippers barricading themselves inside the mosque amid what appeared to be clouds of tear gas.
The Palestinian Red Crescent emergency service said it evacuated 59 wounded people to hospitals. The endowment said one of the guards at the site was shot in the eye with a rubber bullet.
Israeli police said they entered the compound, the third holiest site in Islam and revered by Jews as the Temple Mount, to break up a “violent” crowd that remained at the end of the morning prayers.
They said they went in “to disperse and push back” the crowd after a group of Palestinians began throwing rocks towards the nearby Jewish prayer space of the Western Wall.
Tensions have escalated in recent weeks. Israel has been carrying out arrests and military raids in the illegally occupied West Bank, in the wake of a series of deadly attacks by Palestinians inside Israel, setting off clashes in which several Palestinians have been killed, including seven since Wednesday.
Tens of thousands of Palestinians were expected to gather at Al-Aqsa for Friday prayers, as Muslims observe the holy month of Ramadan.
Weeks of protests and clashes on Al-Aqsa during Ramadan last year escalated into an 11-day war on the besieged Gaza Strip.
Ramadan this year coincides with the Jewish Passover holiday and Christian holy week, bringing thousands of pilgrims and other visitors to Jerusalem.