The Islamic endowment that runs the site said Israeli police entered in force before dawn on Friday, 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 the majority of the wounded to hospitals. The endowment said one of the guards at the site was shot in the eye with a rubber bullet.
The Palestinian Red Crescent added that Israeli forces had hindered the arrival of ambulances and paramedics to the mosque, as Palestinian media said dozens of injured worshippers remained trapped inside the compound.
Israeli police said they arrested at least 300 Palestinians during the latest escalation. However, Palestinian sources put the number at 400.
They said they went in “to disperse and push back” the crowd after a group of Palestinians began throwing rocks toward the nearby Jewish prayer space of the Western Wall.
But Palestinian cameraman, Rami al-Khatib, who witnessed the raid, said: ”They [Israeli forces] brutally emptied the compound. They were attacking the mosque staff, normal people, elders, and young people.
“There were many injured people, they fired rubber bullets inside the Al-Aqsa Mosque compound. They were beating everyone, even the paramedics, they hit them,” said al-Khatib, who too was injured.
Reporting from Damascus Gate, Al Jazeera’s Najwan al-Samri said Israeli police stormed the mosque compound without pretext and assaulted worshippers near the Qibly prayer hall following the morning prayer.
She added that the escalation came as far-right Jewish groups called for raids of the Al-Aqsa Mosque compound during the Jewish Passover holiday, and the offering of animal sacrifices in its courtyards, which has not occurred since ancient times.
Al Jazeera’s senior political analyst Marwan Bishara blamed the Israeli occupation, the “international community’s indifference to Palestinian suffering” amid the Ukraine crisis, and the “paralysis of the Palestinian leadership” as reasons behind the latest developments in Jerusalem.