Patrick Shanahan, a former Boeing executive with no other government experience, is now the nation’s longest-serving acting secretary of defense in history, having taken on the role after James Mattis resigned in December. Some believed that Shanahan’s “acting” prefix would soon give way to a formal appointment to the job, but that effort has been delayed by an investigation launched by the Pentagon’s Office of Inspector General spurred by allegations of favoritism for Shanahan’s previous employer.

The investigation was prompted by a formal complaint filed by the Citizens for Responsibility and Ethics in Washington (CREW), a Washington D.C.-based watchdog group that asserts Shanahan has used his position to promote Boeing within the Department of Defense (DOD), seemingly to the detriment of Boeing’s competitor and F-35 manufacturer, Lockheed Martin. This alleged bias, according to CREW, has manifested in a number of ways, including the Pentagon pressuring the Air Force to procure new F-15 airframes from Boeing.

The CREW complaint states:

Mr. Shanahan worked for Boeing for more than 30 years before joining DOD in 2017. In private remarks he made since then at DOD, Mr. Shanahan reportedly praised Boeing in discussions about government contracts, said that Boeing would have done much better than its competitor Lockheed Martin had it been awarded a fighter jet contract, and repeatedly “dumped on” the jet Lockheed produced. News reports also asserted Mr. Shanahan prodded DOD to include funding for more Boeing-produced fighter jets in next year’s budget. His conduct and comments reportedly were perceived by DOD employees as ‘boosting’ Boeing.

Boeing has secured a number of large defense contracts in recent years, including a $4 billion Super Hornet upgrade contract, a contract to produce the Navy’s new MQ-25 drone refueler, and the forthcoming F-15EX procurement. In fact, in a single month (last September), Boeing secured more than 20 contracts with a total cumulative value of $13.7 billion. It prompted some to contend Boeing has been given the inside track thanks to its man inside: Patrick Shanahan.

The DOD, however, contends Shanahan has welcomed the investigation and has not exerted any undue force on any Boeing or other procurement programs. Lockheed Martin did see a slight downturn in F-35 orders projected for the 2020 fiscal year, something some were keen to blame on new F-15 purchases. However, reports alleging the F-35 continues to face woefully low readiness rates and extremely high maintenance costs that have emerged throughout this controversy suggest Lockheed’s troubles may, at least in part, be of its own making.

“Shanahan has at all times remained committed to upholding his ethics agreement filed with the DOD,” spokesman Army Col. Joseph Buccino told reporters. “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 with Boeing.”