They removed Palestinian flags that were hung to the south of the Dome of the Rock, the Middle East Monitor reported.
Local sources told the media that the occupation forces stormed the mosque "at dawn and confiscated a banner that was hanging on a pillar," adding that soldiers had failed to "lower a Palestinian flag that was hanging on the same pillar."
Since the start of the holy month of Ramadan, Israeli forces have been storming Al-Aqsa, attacking Palestinian worshippers with rubber-coated steel bullets, and arresting hundreds of them.
The attacks have been widely condemned by Muslim, Arab and international governments and leaders.