Boeing declined to comment. A Justice Department spokesman also declined to comment. Alaska Airlines said in a statement Saturday that it was cooperating with the investigation.

“In an event like this, it’s normal for the DOJ to be conducting an investigation,” Alaska Airlines said. “We are fully cooperating and do not believe we are a target of the investigation.”

Spirit AeroSystems, a Boeing supplier that initially installed a panel that came off the jet in midair, said it has received requests for information from “multiple government agencies” and was cooperating with ongoing investigations.

The inquiry comes as an audit by the Federal Aviation Administration identified multiple instances where Boeing failed to comply with quality control requirements in its manufacturing process, an unwelcome reminder of safety problems that led to a 20-month grounding of the fleet following two fatal crashes involving 737 Max 8 jetliners in 2018 and 2019.

The Justice Department is investigating whether any factors that contributed to the Jan. 5 incident violated the terms of an earlier agreement with Boeing to resolve any criminal liability for the two crashes involving 737 Max jets, according to a person familiar with the probe.

Boeing reached that deal with the Justice Department in 2021 over employees’ concealment of a critical safety flaw implicated in crashes that killed 346 people in Ethiopia and Indonesia. Boeing agreed to pay more than $2.5 billion in penalties and admitted that two of its technical pilots deceived federal safety regulators about a software system blamed for the accidents.

As part of the agreement, Boeing would avoid criminal prosecution if it met other conditions for a period of three years, including promptly reporting any evidence that its employees or agents committed fraud against any government agencies, regulators or its customers. The company also agreed to strengthen its compliance program and to enhance compliance program reporting requirements.

The deal, known as a deferred prosecution agreement, also required Boeing to fully cooperate with any investigation by the fraud section of the Justice Department’s criminal division, including turning over upon request any evidence or allegations of violations or any related internal or external investigations.

The Justice Department stopped short of requiring the appointment of an independent monitor to ensure Boeing’s compliance, however, saying it did not believe one was needed.

Paul G. Cassell, a lawyer representing some families of victims in the 2018 and 2019 crashes, said a series of issues at Boeing over the past year raise questions about whether it has complied with the terms of the agreement.

“It’s not just one door plug on one plane,” said Cassell, a professor at the University of Utah College of Law.

Whether the causes of the door plug incident constitute a violation that 2021 agreement or lead to the discovery of new alleged offenses, or some combination of the two, appears to be an open question. The Justice Department’s criminal division has until July 7 to decide whether to seek dismissal of the 2021 charges against Boeing, extend the probationary term by up to one year, or find the company in breach of the settlement. Such a finding could reactivate the prosecution.

Boeing is already the target of multiple investigations following the Jan. 5 blowout.

The FAA has stepped up oversight of its manufacturing and quality control processes. The agency also has taken the unusual step of limiting the number of aircraft the company can produce until it can be assured that Boeing has addressed the problems that contributed to the Alaska Airlines blowout.

FAA Administrator Michael Whitaker recently visited Seattle, a trip that included a tour of Boeing’s 737 production line. He also spoke with Boeing engineers and mechanics as well as FAA employees tasked with oversight of the company.

On Monday, the FAA said it had completed the audit and found multiple instances of Boeing and Spirit failing to adhere to quality control requirements. The agency said it has given Boeing 90 days to develop a plan to correct the problems.

According to the National Transportation Safety Board’s preliminary findings in the Jan. 5 incident, the door plug appeared intact when it left Spirit AeroSystems on Aug. 20. However, a photo shared by Boeing employees on Sept. 19 after it was removed for a repair shows three of four key bolts missing, with a fourth not visible in the picture.

Boeing said in a letter Friday to Sen. Maria Cantwell (D-Wash.) that it has searched for documentation about the removal of the part but has not discovered any records.

“We likewise have shared with the NTSB what became our working hypothesis: that the documents required by our processes were not created when the door plug was opened,” the company wrote. “If that hypothesis is correct, there would be no documentation to produce.”