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President Trump on Tuesday withdrew the nomination of Patrick M. Shanahan to be the permanent defense secretary, leaving the Pentagon in transition at a time of escalating tensions with Iran and questions about the role of the military at the border with Mexico.

Mr. Shanahan, who had been serving as the acting defense secretary, announced his resignation as a routine F.B.I. background investigation, conducted on all cabinet nominees, was continuing because of Mr. Shanahan’s divorce. Mr. Shanahan’s ex-wife had accused him of punching her in the stomach, which Mr. Shanahan has denied. He said that his ex-wife started the fight, and his spokesman said that she was arrested and charged with domestic violence, charges which were eventually dropped.

Mr. Trump named Mark T. Esper, the secretary of the Army and a former Raytheon executive, to take over as acting secretary of defense. He did not say whether Mr. Esper would be nominated for the permanent position.

The move leaves the Pentagon leader at a time of escalating tensions with Iran after attacks on oil tankers in the Persian Gulf. The Trump administration has blamed Iran for the explosions that damaged the two tankers.

In a Twitter post, the president said the withdrawal was the decision of Mr. Shanahan, who has served for six months as acting defense secretary. But it is the president’s prerogative to withdraw the nomination.

Acting Secretary of Defense Patrick Shanahan, who has done a wonderful job, has decided not to go forward with his confirmation process so that he can devote more time to his family....
— Donald J. Trump (@realDonaldTrump) June 18, 2019

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Mr. Trump’s decision not to move ahead with Mr. Shanahan is the latest evidence of the difficulty that the president has had in permanently filling the top jobs in his administration.

The president also has an acting chief of staff at the White House and an acting secretary of homeland security.

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The White House reportedly looked into demoting Federal Reserve Chairman Jay Powell in February, a few months after the central bank last hiked interest rates.

Bloomberg reported Tuesday that the White House Legal Counsel examined whether it was possible to strip Powell of his chairmanship but keep him on the Federal Reserve Board of Governors. President Donald Trump handpicked Powell to lead the central bank in 2017.

White House economic adviser Larry Kudlow said Tuesday that the administration was not taking action to change Powell's status. Asked for comment on the Bloomberg report, a different White House official said: "We're not going to comment on alleged conversations from 6 months ago that are not being pursued or considered."

Trump has repeatedly lambasted the Federal Reserve, arguing that its policies have held back growth. Ahead of the 2020 elections, he has increased pressure on independent central bank to lower interest rates and has sought to put political allies on its policymaking board.

In December, Bloomberg reported that Trump had discussed firing Powell shortly after the Federal Open Market Committee increased its benchmark interest rate to a target range of between 2.25% and 2.5%. But it was unclear whether that move would have been legal, and Powell has said he would not resign if the president asked him to.