Israeli police entered the flashpoint Al-Aqsa mosque compound on Sunday after Palestinians threw stones at visitors, Agence France-Presse repports.
"Muslim worshippers threw stones at visitors to the site today, and our forces have entered to make arrests," spokesman Micky Rosenfeld told the French news service.
"Around 20 young people are holed up inside the mosque, and as a preventive measure we have decided to limit access to the esplanade to men over the age of 50," as well as women and children, he added.
Dozens of riot police were deployed throughout the narrow streets of the Old City as loudspeakers on minarets called on Muslims to "save Jerusalem," according to an AFP correspondent.
An official from Jerusalem's Islamic Supreme Committee said the Palestinians threw stones at people they believed to be Jewish extremists intending to pray at the site and upset the delicate status quo.
"They threw rocks because (Israeli) settlers have been surrounding the compound for two or three days and had said they intended to enter on Sunday or Monday to pray at Al-Aqsa," Adnan Husseini told AFP.