The official Palestinian news agency Wafa reported that dozens of mosque-goers were injured in the police operation.
The incident led to a wave of Palestinian protests and condemnation of the violence. In Gaza, the Islamist movement Hamas called for protests.
According to Israel’s military, air strikes warning of incoming rockets have been heard in Israeli communities near the Gaza Strip.
It is not yet clear what triggered the violence at the mosque. The Israeli police state that they used violence to get people out of the mosque with fireworks, stones and sticks. A policeman was reportedly hit by a rock and injured, and dozens of Palestinians were reportedly arrested.