Israeli police were questioning Jerusalem's most senior Muslim cleric on Wednesday for suspected involvement in a "disturbance" at the Al-Aqsa mosque compound in the Holy City, a spokesman said.

Mufti of Jerusalem Mohammed Hussein was taken from his home by detectives and was being questioned at a police station "on suspicion of involvement in a disturbance that took place yesterday (Tuesday) on Temple Mount," police spokesman Micky Rosenfeld said.

"Some chairs were thrown at a group of Jews on the Temple Mount," which Muslims refer to as Al-Haram Al-Sharif, Rosenfeld told AFP of the previous day's incident.

The contested site, which overlooks the Western Wall plaza, houses both the Dome of the Rock and Al-Aqsa mosques, and is venerated by Jews as the site where their ancient temples stood before the Second Temple was destroyed by the Romans in 70 AD.

Hussein's detention comes on Jerusalem Day, when Israel marks the "reunification" of the city after it captured the Arab eastern sector from Jordan during the 1967 Six-Day War.

Israel later annexed east Jerusalem in a move never recognised by the international community.

Thousands of Israelis will hold marches and rallies throughout the city later on Wednesday, and Rosenfeld said "thousands of police were being deployed in and around Jerusalem and the Old City in preparation for the annual events."