Masked youths discharged fireworks in the direction of Israeli police near Jerusalem's most important mosque on Friday and police charged the mosque compound to confront them, Reuters Television footage showed.
It was not immediately clear if the entry of the police happened before or after the fireworks.
An Israeli police spokesman said firecrackers and stones were lobbed at police at the mosque compound "for an unknown reason". Police were clearing the compound in response, he said.
The compound, which Jews also revere as vestige of their two ancient temples, is a frequent flashpoint of Israeli-Palestinian tensions.
The waqf, the religious authority that runs the mosque, confirmed the gates were closed after clashes broke out.
#BREAKING Clashes erupted between #Israel|i police and Muslim prayers in Al-Aqsa mosque, #Jerusalem pic.twitter.com/NtUmZoZar8
— Guy Elster (@guyelster) July 27, 2018