WASHINGTON — The Trump administration is coming under increasing pressure to nominate someone to lead the Pentagon, nearly three months after President Donald Trump’s first secretary of defense, Jim Mattis, resigned in a policy dispute.

Patrick Shanahan, who has been the acting secretary since Mattis left Dec. 31, was thought to be Trump’s likely choice for the nomination. But expectations have become clouded in recent weeks, in part by the launching of a Defense Department watchdog investigation of alleged Shanahan bias in favor of his former longtime employer, Boeing Co., which is a major defense contractor.

It is highly unusual for the Pentagon to be led by an acting secretary. Shanahan is only the third person to perform the job in that capacity since the Defense Department was created in 1947. It is less uncommon elsewhere in government, and Trump has an outsize number of Cabinet secretaries and other advisers with "acting" in their titles.

In the case of the Defense Department, the absence of a confirmed secretary is a sore point with the Senate.

"We need to have a nominee for the secretary of defense, and I would like to see that nomination come from the White House soon," Sen. James Inhofe, the Republican chairman of the Senate Armed Services Committee, said Tuesday.

Acting Defense Secretary Patrick Shanahan, center, and David Norquist, far right, the Defense Department's budget chief, arrive to testify at a House Armed Services Committee hearing on the fiscal year 2020 Pentagon budget, on Capitol Hill in Washington, Tuesday, March 26, 2019. (J. Scott Applewhite/AP)
Acting Defense Secretary Patrick Shanahan, center, and David Norquist, far right, the Defense Department's budget chief, arrive to testify at a House Armed Services Committee hearing on the fiscal year 2020 Pentagon budget, on Capitol Hill in Washington, Tuesday, March 26, 2019. (J. Scott Applewhite/AP)

Inhofe's House counterpart, Rep. Adam Smith, a Washington state Democrat, tried to inject a little humor into the awkward circumstance facing Shanahan. With Shanahan seated at the House Armed Services Committee witness table, preparing to testify on the administration's 2020 defense budget request, Smith said "there's getting to be sort of a Bud Selig joke here." He was referring to Selig serving as interim commissioner of major league baseball for six years before finally being named the official commissioner.

"We are hoping that doesn't happen in your case as well," Smith said.

In a statement provided by his office, Inhofe also said that if Trump nominates Shanahan, there should be a “thorough but expeditious examination of any outstanding issues” by the Defense Department inspector general. That appeared to be a reference to the inspector general opening an investigation last week into a complaint by Citizens for Responsibility and Ethics in Washington that Shanahan has used his office to promote Boeing.

Shanahan has welcomed the IG review and said through a spokesman that he has scrupulously upheld his ethics agreement with the Defense Department. That agreement, signed in June 2017 shortly before Shanahan was confirmed by the Senate as deputy secretary of defense, is designed to avoid any actual or perceived conflict of interest. It says Shanahan will recuse himself from decisions involved Boeing business.

Shanahan, a native of Washington state, worked for Boeing for 31 years.

Separately, the Pentagon said Tuesday that Trump has nominated Air Force Gen. John W. Raymond to serve as commander of the new U.S. Space Command, which is being created as part of the administration's efforts to improve the nation's space defenses. Raymond currently is commander of Air Force Space Command, which eventually will become subordinate to U.S. Space Command.

Trump also nominated Gen. James McConville to become Army chief of staff, succeeding the current chief, Gen. Mark Milley, who has been nominated to be the next chairman of the Joint Chiefs of Staff. McConville currently is the Army's vice chief of staff.

Associated Press writer Lolita C. Baldor contributed to this report.