WASHINGTON — The Defense Department’s inspector general said on Wednesday that it was investigating complaints that the acting defense secretary, Patrick M. Shanahan, had been promoting his former employer, the Boeing Company, and disparaging its military contractor competitors.

The investigation will examine complaints filed last week by a watchdog group, Citizens for Responsibility and Ethics in Washington. Dwrena K. Allen, a spokeswoman for the inspector general’s office, said that investigators had informed Mr. Shanahan of the inquiry.

Mr. Shanahan told lawmakers last week that he supported an investigation.

The investigation complicates what is already an uphill battle for Mr. Shanahan’s effort to become the next permanent defense secretary. As recently as last week, Defense Department officials believed that President Trump was about to formally nominate Mr. Shanahan for the job left vacant by Jim Mattis, who resigned in December.

But as Mr. Shanahan’s troubles mount, the White House does not appear to have a ready and able alternative to him.

Jim Talent, the former senator of Missouri, is one name which White House officials have discussed, according to former and current administration officials. Also under consideration is Robert L. Wilkie, the Veterans Affairs secretary. But Mr. Wilkie is viewed as doing a good job in a troubled department and Mr. Trump is loath to remove him from his post, the officials said.

The deadly crash of a Boeing 737 Max 8 jet in Ethiopia, along with growing complaints that his cozy relationship with his former employers at the detriment of other military contractors, puts Mr. Shanahan’s fate in limbo.

Mr. Shanahan served as the Pentagon’s deputy secretary under Mr. Mattis, a job that required Senate confirmation. Before that, he spent 30 years in commercial aviation and business at Boeing. He had hoped to bring his reputation as a corporate problem solver — including helping introduce the 787 Dreamliner — to the Defense Department.

Several Defense Department officials predicted this week that it was unclear whether Mr. Shanahan could win Senate confirmation for the Pentagon’s top job, given his longstanding ties with Boeing and the fallout from the crash of the Ethiopian Airlines plane.

The transportation secretary, Elaine L. Chao, called on Tuesday for her agency’s internal watchdog to investigate the process by which the Federal Aviation Administration in 2017 approved designs for the 737 Max. Lawmakers in Congress also are pushing for a review, while Canada is looking into its approval of the plane’s American certification.

The specific allegations that the Defense Department’s inspector general is examining revolve around complaints, first reported in Politico, that Mr. Shanahan disparaged competitors of Boeing during meetings at the Pentagon with senior national security officials and lawmakers, two United States officials said.

Senator Elizabeth Warren, Democrat of Massachusetts and a member of the Armed Services Committee that would consider Mr. Shanahan’s confirmation if he is nominated, said she alerted the Pentagon’s internal watchdog after hearing that he “may have advocated on behalf of his former employer, Boeing, while serving as the acting defense secretary.”

“The American people should be able to trust that government officials are working for them — not for big defense contractors,” Ms. Warren, who is running for president, said in a statement.

While Mr. Mattis resigned in protest of Mr. Trump’s policies — including the surprise announcement that American troops would withdraw from Syria — Mr. Shanahan has held the line for the president.

As the deputy defense secretary, Mr. Shanahan made clear that “we are not the Department of No,” as he told officials after the administration announced plans to create a new stand-alone Space Force at the Pentagon. It has since been moved to the oversight of the Air Force.

Since becoming acting defense secretary, Mr. Shanahan has raised the ire of some lawmakers. Last month, Senator James M. Inhofe, Republican of Oklahoma and the chairman of the Armed Services Committee, said he did not believe Mr. Shanahan shared the “humility” of Mr. Mattis but did not elaborate. Senator Lindsey Graham, Republican of South Carolina, also clashed with Mr. Shanahan last month over the planned troop withdrawal from Syria.

Last week, Mr. Shanahan appeared in front of Mr. Inhofe’s committee to sell the Pentagon’s proposed $750 billion budget for the 2020 fiscal year, which is geared toward combating threats from Russia and China and modernizing a military that has long focused on counterinsurgency conflicts.

Instead, senators accosted him on a range of issues, including Mr. Trump’s move to take billions of dollars from the Defense Department for a border wall, and the Pentagon’s decision to push for weaker standards on chemicals in drinking water.

Eric Schmitt contributed reporting.

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