Palestinians say police entered the Al-Aqsa mosque causing damange, and used tear gas and stun grenades outside the complex.
Israeli police say they came in to prevent rioters who were throwing stones and fireworks in a bid to disrupt celebrations to mark the start of the Jewish New Year. It's not being reported that the police have cleared the area of those they believed had caused the disturbance.
The mosque is sacred to both faiths, and is in fact the third most-holy Islam site - but last week the Israeli Defence Minister banned two Muslim groups from visiting the site on security grounds.
Non-Muslims are allowed to visit the compound, but Jews are forbidden from praying or displaying national symbols for fear of triggering tensions with Muslim worshippers.