A number of videos released on social networks showed images of the Israeli police assault on the Al Aqsa Mosque, which is part of the religious complex.
During the operation, the Israeli soldiers broke down one of the entrance doors and caused damage to the ancient site.
The soldiers used rubber bullets and tear gas against the faithful, who in turn chanted slogans against the occupation. Palestinian media reported clashes in the courtyard.
Both the Imam of the Mosque, Sheikh Ikrima Sabri, and its director, Sheikh Omar Al-Kiswani, condemned the attack by Tel Aviv troops.
The Popular Front for the Liberation of Palestine called for intensifying the resistance in the occupied territories.
The raid was aimed at escorting hundreds of Jewish settlers, divided into at least eight groups, who were waiting outside while the police cracked down on the Palestinians, into the religious complex.