Israeli police forces have stormed a disputed Jerusalem holy site to stop Palestinian rioters from throwing stones at Jewish worshippers.

Police on Wednesday briefly moved onto the hilltop compound, known to Jews as the Temple Mount and to Muslims as the Noble Sanctuary, and took up positions.

The site is the most explosive in the Israeli-Palestinian conflict, and in the past, even seemingly minor incidents have ignited clashes and protests throughout the region.

Police spokesman Micky Rosenfeld says the stone throwers fled into the Al Aqsa Mosque, and after the situation quieted, riot forces pulled back.

Palestinian youths have been clashing with police throughout the day following the deadly shooting of a Palestinian man by an Israeli security guard.