The settlement is stopped because the judge is dissatisfied with the criteria set by the department for the selection of the independent observer who is to ensure that the company follows the rules.
In July, Boeing agreed to plead guilty to having attempted to deceive the US government by misleading regulatory authorities about a flight control system on board Boeing 737 Max aircraft, which were later involved in the accidents.
This concerns the two plane crashes in Indonesia and Ethiopia in 2018 and 2019, which together claimed 346 human lives.
Boeing and the Justice Department now have 30 days to decide how to proceed. They have not yet commented on the federal judge's decision.