The abuses include "torture and other cruel, inhuman or degrading treatment or punishment," the EU Council said in a statement.
Dozens of Orthodox Jews attempted to interrupt the event and rioted, with one of them being arrested for allegedly attacking an policeman.
The report alleged that far-right activist Benzi Gopstein had been advising the national security minister on police matters.
Bentzi Gopstein was banned from running for Knesset in 2019 as he was indicted on charges of incitement to terrorism, violence and racism.
On Monday, the far-right Lehava organization called on supporters of the organization to join a protest against the march, stating "Jerusalem is not Sodom!"
As rioters chased the taxi, the driver hit a pedestrian's leg.