Local sources, speaking on condition of anonymity, said Israeli troops entered in force before dawn on Friday, as thousands of worshipers gathered at the mosque for early morning prayers.
The sources added that Israeli soldiers fired tear gas and stun grenades as worshipers barricaded themselves inside the mosque amid what appeared to be clouds of tear gas.
Palestinian media said at least 43 Palestinians were injured in the raid.
The development comes a day after as many as 30 Palestinians were wounded after Israeli forces continued their violent attacks against worshipers at the al-Aqsa Mosque compound in occupied al-Quds, Press TV reported.
“One person was transferred to hospital with a rubber bullet (wound) to his back,” medical sources were quoted as saying.
The troops used rubber bullets, tear gas canisters, stun grenades, and pepper spray against the worshipers, who have been braving increasing aggression ordered by the Israeli regime since the beginning of the holy month of Ramadan.
Palestinians returned the violence by throwing stones and Molotov cocktails.
In their most serious bout of aggression against the Palestinians during Ramadan, Israeli forces injured more than 150 worshipers at the compound last Saturday.