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Acting U.S. defence secretary Patrick Shanahan speaks at the Center for Strategic and International Studies in Washington on March 20, 2019.Andrew Harnik/The Associated Press

The Pentagon’s inspector-general has formally opened an investigation into a watchdog group’s allegations that acting U.S. Defence Secretary Patrick Shanahan has used his office to promote his former employer, Boeing Co.

Citizens for Responsibility and Ethics in Washington (CREW) filed an ethics complaint with the Pentagon’s inspector-general a week ago, alleging that Mr. Shanahan has appeared to make statements promoting Boeing and disparaging competitors, such as Lockheed Martin Corp.

Mr. Shanahan, who was travelling with U.S. President Donald Trump to Ohio on Wednesday, spent more than 30 years at Boeing, leading programs for commercial planes and missile-defence systems. He has been serving as acting Pentagon chief since the beginning of the year, when James Mattis stepped down.

The probe comes as Boeing struggles to deal with a public firestorm over two deadly crashes of the Boeing 737 Max 8 passenger jet within the last five months. And it focuses attention on whether Mr. Trump will nominate Mr. Shanahan as his formal pick for defence chief, rather than letting him languish as an acting leader of a major federal agency.

Dwrena Allen, spokeswoman for the inspector-general, said Mr. Shanahan has been informed of the investigation. In a statement, Pentagon spokesman Tom Crosson said Mr. Shanahan welcomes the review.

“Acting Secretary Shanahan has at all times remained committed to upholding his ethics agreement filed with the DoD,” Mr. Crosson said. “This agreement ensures any matters pertaining to Boeing are handled by appropriate officials within the Pentagon to eliminate any perceived or actual conflict of interest issue(s) with Boeing.”

During a Senate hearing last week, Mr. Shanahan was asked by Senator Richard Blumenthal, a Connecticut Democrat, about the 737 Max issue. Mr. Shanahan said he had not spoken to anyone in the administration about it and had not been briefed on it. Asked whether he favoured an investigation into the matter, Mr. Shanahan said it was for regulators to investigate.

On Wednesday, Mr. Blumenthal said that scrutiny of Mr. Shanahan’s Boeing ties is necessary. “In fact, it’s overdue. Boeing is a behemoth 800-pound gorilla – raising possible questions of undue influence at DOD, FAA and elsewhere,” the senator said.

Mr. Shanahan signed an ethics agreement in June, 2017, when he was being nominated for the job of deputy defence secretary, a job he held during Mr. Mattis’s tenure. It outlined the steps he would take to avoid “any actual or apparent conflict of interest,” and said he would not participate in any matter involving Boeing.

The CREW ethics complaint, based to a large part on published reports, said Mr. Shanahan has made comments praising Boeing in meetings about government contracts, raising concerns about “whether Shanahan, intentionally or not, is putting his finger on the scale when it comes to Pentagon priorities.”

One example raised by the complaint is the Pentagon’s decision to request funding for Boeing 15EX fighter jets in the 2020 proposed budget. The Pentagon is requesting about US$1-billion to buy eight of the aircraft.

Mr. Shanahan, 56, joined Boeing in 1986, rose through its ranks and is credited with rescuing the once-troubled Dreamliner 787 program. He also led the company’s missile-defence and military-helicopter programs.

Mr. Trump has seemed attracted to Mr. Shanahan partly for his work on one of the President’s pet projects – creating a Space Force. He also has publicly lauded Mr. Shanahan’s former employer, Boeing, builder of many of the military’s most prominent aircraft, including the Apache and Chinook helicopters, the C-17 cargo plane and the B-52 bomber, as well as the presidential aircraft, Air Force One.

This is only the third time in history that the Pentagon has been led by an acting chief, and Mr. Shanahan has served in that capacity for longer than any of the others.

Presidents typically take pains to ensure the Pentagon is being run by a Senate-confirmed official, given the grave responsibilities that include sending young Americans into battle, ensuring the military is ready for extreme emergencies such as nuclear war and managing overseas alliances that are central to U.S. security.

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