Eyewitnesses told Al Jazeera that the confrontation between Israeli forces and Palestinians began on Sunday after officers entered the compound.
Israeli forces used stun grenades and rubber-coated steel bullets against the Palestinians.
It doesn't appear as if the clashes went far beyond the gate where police entered, nor are there reports of any injuries, Al Jazeera said.
These confrontations at the al-Aqsa Mosque come at a very tense time. Over the past several days, there have been frequent confrontations between Israeli security forces and Palestinian worshippers, who go to the site.
In a statement to Al Jazeera, Asi Aharoni, Jerusalem police spokesperson, confirmed the report.
In recent days, during the Jewish new year of Rosh Hashana, there were also clashes, which damaged parts of the mosque, Islam's third holiest site.
Efforts by Israeli police to allow Jewish activists to tour the courtyards of the mosque have stirred strong reactions from Palestinians who fear Israel may change the rules for visiting the compound.