Police fired tear gas and rubber bullets at a group of Palestinian youths on Sunday as clashes broke out at the contested plaza in Jerusalem.
According to police, Palestinians barricaded themselves in the mosque overnight in protest over members of the Jewish far right visiting the site to commemorate a Jewish holy day.
The mosque is revered by Muslims as the Noble Sanctuary and by Jews as the Temple Mount where two biblical temples once stood. Yesterday marked the annual Jewish day of mourning, Tisha B'Av, for the destruction of the temples.
Non-muslims are allowed to visit the site as part of guided tours, but they are not allowed to pray. Ultranationalist Jews have in recent years upped their calls for this law to be revoked amid rising tensions between Jewish and Muslim groups.
CNN reports that Israeli police released a video showing rocks and other objects being thrown from the mosque, purportedly by the group of Palestinians. "Masked rioters fled into the mosque and started to throw stones and blocks at police from inside Al-Aqsa Mosque. They threw fireworks directly at police," a police statement said.
"In view of the harsh confrontation and escalation of the actions of the rioters and in order to prevent further injury to policemen ... the force entered a few metres inside, managed to close the doors of the mosque with the rioters inside, [and] restored peace."
However, Sheikh Omar Kisswani, the general director of al-Aqsa, gave CNN a different version of events. He said that Israeli police "raided" the mosque, using weapons including stun grenades and rubber bullets. Kisswani added that more than 12 Palestinian worshippers were injured in the clashes, including one who was badly beaten.
A correspondent for Aljazeera confirmed that police fired sound bombs within the compound, while the Times of Israel attributed rising tensions to an incident last Thursday when a right-wing Jewish activist insulted Mohammed in front of Muslims.
Israeli president Reuven Rivlin condemned Sunday's incident. "The acts of violence and terrorism committed – especially today – against worshipers at holy sites must be condemned unequivocally," he said.
"I express my support for the security forces and for their determination to prevent any harm or interference to the prayers at the Western Wall, the remnant of our Temple. Such acts of hatred cannot be tolerated, and we will not allow any disturbances to prevent Jews from praying at this holy site."