Israeli police said they would bar men under 50 from Friday Muslim prayers at Jerusalem's Al-Aqsa compound after Israel removed security devices installed following a shootout.

"Security assessments were made and there are indications that disturbances and demonstrations will take place today," police said in a statement of the Haram al-Sharif compound, known to Jews as the Temple Mount.

"Only men over the age of 50 will be permitted and women of all ages are permitted. A number of roads around the Old City will be limited to access and all necessary security measures are being taken to prevent and to respond to any outbreak of violence."

The site includes the Al-Aqsa mosque and the Dome of the Rock.

On Thursday, Palestinians ended a boycott of the site over new Israeli security measures there and entered for the first time in two weeks.

Thousands of worshippers streamed into the site on Thursday afternoon. Clashes between Israeli police and Palestinians erupted soon after, with the Palestinian Red Crescent reporting around 100 people wounded.

Israel removed the security devices amid intense pressure by Muslims around the world and said it plans to install sophisticated security cameras instead.

Jerusalem is sacred to Muslims, Jews and Christians, and the Al-Aqsa Mosque is considered to be the third holiest site for Muslims, after the Kaaba in Mecca and al-Masjid an-Nabawi in Medina.