Israeli forces stormed al-Aqsa mosque compound on Sunday, firing rubber-coated bullets at "rioters" amid fresh clashes at the flashpoint site, police said.
Masked Palestinian youths "threw stones and firecrackers at police and Border Police forces" who responded with "riot dispersal means", Xinhua news agency quoted a police spokesman as saying.
The police also used rubber-coated bullets to push people back into the mosque.
The situation is currently "under control", the spokesperson said.
Tensions in and around the holy compound have been running high in recent weeks with Jews marking their High Holidays. Sunday was also the last day of the three-day Muslim holiday of Eid al-Adha.
Al-Aqsa compound is the third holiest site in Islam and the holiest site for Jews who know it as the Temple Mount and revere it as the site of their second temple, which was destroyed in 70 AD.
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Israel's Defence Minister Moshe Ya'alon said all Muslim residents of east Jerusalem would be allowed full access to the site and entry for the Jews will be restricted to avoid clashes.
Visits to the site by Israeli far-right activists have been on the rise, as part of their struggle to cancel a long-held ban on Jewish prayers there.
Palestinians say Israel is violating a status quo agreement from 1967, which allow Jews to visit the site but prohibit them from praying.