A US judge in December rejected the deal, faulting a diversity and inclusion provision, and Boeing and the Justice Department have been negotiating toward a new agreement.
US President Donald Trump took over on January 20, giving his administration a chance to weigh in on the deal.
Boeing declined comment. The Justice Department did not immediately comment.
In July, Boeing agreed to plead guilty to a criminal fraud conspiracy charge in the wake of two fatal 737 MAX crashes.
The planemaker also agreed to pay a fine of up to $US487.2 million ($A773.5 million) and spend $US455 million ($A722 million) to improve safety and compliance practices over three years of court-supervised probation as part of the deal.
Relatives of the victims of the two 737 MAX crashes, which occurred in 2018 and 2019 and killed 346 people, have called the plea agreement a "sweetheart" deal that failed to adequately hold Boeing accountable for the deaths of their loved ones.
An accepted plea deal would brand Boeing a convicted felon for conspiring to defraud the US Federal Aviation Administration about problematic software affecting the flight control systems in the planes that crashed.
In May, the DOJ found Boeing had violated the terms of a 2021 agreement that had shielded it from prosecution over the crashes. Prosecutors then decided to criminally charge Boeing and negotiate the current plea deal.
The decision followed a January 5, 2024, in-flight blowout of a door panel on an Alaska Airlines' jet that exposed ongoing safety and quality issues at Boeing.
Judge Reed O'Connor in Fort Worth, Texas in 2023 said "Boeing's crime may properly be considered the deadliest corporate crime in US history."
Trump administration officials have said regulators must be firm with Boeing after a series of missteps.
"We need to be tougher on Boeing. We need to be tougher on the industry," said Steve Bradbury, who was confirmed as deputy transportation secretary this month.
Boeing on Friday won a contract to build the US Air Force's most sophisticated fighter jet yet.
