The clashes erupted after several dozen masked Palestinians began throwing rocks, fire crackers and other pyrotechnical devices at police when the Temple Mount, known to Muslims as the "Noble Sanctuary," opened for prayers on Wednesday morning, said the spokeswoman, Luba Samri.
There was no immediate information on whether anyone was hurt among the Palestinian protesters.
Police chased the demonstrators toward the Al-Aqsa mosque, where they barricaded themselves inside and continued hurling objects in the direction of the police, said Samri. She said that at least one Molotov cocktail was thrown at the police, but that it failed to ignite.
The Temple Mount is the holiest site in Judaism and the third holiest in Islam, and is a frequent flashpoint for demonstrations.
An Israeli Tourism Ministry decision earlier this week to expand the entrance to the Temple Mount was condemned by Palestinian officials as a unilateral change in the status of the sensitive holy site.