The report from the Office of Special Counsel stems from a whistleblower complaint filed by an air traffic controller at the airport.
Controller Raymond Adams raised safety issues regarding planes landing on intersecting runways at Newark. An investigation found that the procedures posed significant safety risks and needed correction.
The FAA reported it had taken the required steps by late October, but a subsequent investigation revealed it hadn't done so.
The FAA said Wednesday that the new safety measures will be fully implemented by mid-December