Video released by the police showed fireworks exploding and lighting up the prayer hall as heavily armed officers in riot gear moved in.
Other footage posted on social media appeared to show an officer using a rifle butt and others using sticks to beat Palestinians on the floor amid shouts and screams.
Pictures of the aftermath showed overturned furniture and prayer mats scattered across the carpet.
The Palestinian Red Crescent reported that 50 Palestinians were injured. It also said Israeli forces prevented its medics from reaching the mosque, though this has not been confirmed.
Some of the Palestinians still in Israeli custody are in a critical condition, according to their lawyer.