Mr. Hegseth’s inner circle of close advisers — military veterans who, like him, had little experience running large, complex organizations — is in shambles. Three members of the team he brought with him into the Pentagon were accused last week of leaking unauthorized information and escorted from the building.

A fourth recently departed member of Mr. Hegseth’s team, John Ullyot, who had been his top spokesman, accused Mr. Hegseth of disloyalty and incompetence in an opinion essay in Politico on Sunday. “The building is in disarray under Hegseth’s leadership,” Mr. Ullyot wrote.

The discord, according to current and former defense officials, includes: screaming matches in his inner office among aides; a growing distrust of the thousands of military and civilian personnel who staff the building; and bureaucratic logjams that have slowed down progress on some of President Trump’s key priorities, such as an “Iron Dome for America” missile-defense shield. The officials spoke on the condition of anonymity to discuss internal business.

Adding to the dysfunction, Elon Musk’s Department of Government Efficiency has set a loose target of slashing as many as 200,000 jobs from the Pentagon’s civilian work force of 750,000, a level of cuts Mr. Hegseth has warned would cripple some critical functions within the department, three current and former defense officials said.

Elon Musk’s team has set a target of slashing as many as 200,000 jobs from the Pentagon’s civilian work force, a level of cuts that Mr. Hegseth has warned would cripple critical functions.Credit…Valerie Plesch for The New York Times

Meanwhile, recent media reports that Mr. Hegseth disclosed sensitive military information about upcoming strikes in Yemen in two private Signal group chats have led some in Congress to call for him to resign.

Sean Parnell, the Pentagon’s chief spokesman, blamed reports of dysfunction in Mr. Hegseth’s office on “disgruntled former DoD employees with an axe to grind.”

The missteps so far haven’t seemed to shake Mr. Trump’s support for Mr. Hegseth, whom the Senate narrowly confirmed amid concerns about his lack of experience and his drinking.

“This is what happens when the entire Pentagon is working against you and working against the monumental change you are trying to implement,” Karoline Leavitt, the White House press secretary, told Fox News.

Mr. Trump on Monday praised Mr. Hegseth’s work. “He’s doing a great job — ask the Houthis how he’s doing,” the president said, referring to the rebel group in Yemen that the United States has been targeting in military strikes.

Mr. Hegseth similarly defended his brief tenure. Speaking to reporters at the White House Easter Egg Roll on Monday, he accused the news media of using “disgruntled former employees” to smear him and vowed to keep working to put the Pentagon “back into the hands of war fighters.”

Mr. Hegseth has focused much of his energy on restoring a “warrior ethos” to the department, which he said had been taken over by “woke,” diversity-obsessed ideologues. He has dispatched thousands of troops as part of an effort to stem the flow of migrants at the southern border and vowed to better equip the U.S. military to counter a rising China.

Mr. Hegseth during a visit to the U.S.-Mexico border in February.Credit…Paul Ratje for The New York Times

The battles that have roiled Mr. Hegseth’s inner office, though, have focused more on often petty bureaucratic disputes than policy issues, said current and former defense officials. Staff members have complained that meetings overseen by Mr. Hegseth’s handpicked chief of staff, Joe Kasper, meander or take pointlessly bawdy turns.

One meeting Mr. Kasper led this month, with a group that works with veterans that was offering its services to the Pentagon, devolved into a recounting of an evening Mr. Kasper and a representative of the group spent at a Washington strip club, said a person who took part in the session.

Other officials said that Mr. Hegseth and Mr. Kasper had been unable to establish a process to ensure that basic, but essential, matters move swiftly through Mr. Hegseth’s office. In late January, Mr. Trump issued an executive order calling for the fielding and deployment of a missile shield to protect the United States from attacks by adversaries such as North Korea and Iran. At the White House’s urging, Pentagon officials scrambled over the course of a few days to put together a “package” directing the Pentagon’s vast bureaucracy to begin moving forward on the complex project.

The document sat unsigned in the defense secretary’s office for nearly three weeks while White House officials called almost daily to check on its status, current and former defense officials said.

Mr. Hegseth appears to be aware of the problems and is weighing whether to keep Mr. Kasper in his position or replace him with Marine Corps Col. Ricky Buria, according to senior defense officials. Colonel Buria, who served as Mr. Hegseth’s junior military assistant, put in his retirement papers last week, according to the Marines. Defense officials characterized the move as a likely first step toward Colonel Buria taking a senior civilian job in the Pentagon.

The problems inside Mr. Hegseth’s office have been compounded by a growing distrust of civil servants and senior military officials who serve as the Pentagon’s institutional memory.

Some Pentagon officials said that Mr. Hegseth’s team have been combing through their old social media posts and writings, searching for possible signs of disloyalty to Mr. Trump or his movement. Three civilian Pentagon officials said that their bosses had asked them to provide copies of their résumés so they could prove their “patriotism” to Mr. Hegseth’s office. In all three cases, the employees had served in combat; two of them had been wounded in Afghanistan.

The mistrust has extended to senior military leaders who have worked in Democratic and Republican administrations over the course of their decades-long careers.

Mr. Trump fired the chairman of the Joint Chiefs of Staff he inherited, Gen. Charles Brown. And, fearing the potential for leaks, he has kept some generals and admirals from the Joint Staff, who play a key coordinating role, at a distance, defense officials said.

President Trump fired the chairman of the Joint Chiefs of Staff he inherited, Gen. Charles Brown.Credit…Jim Bourg for The New York Times

General Brown’s temporary successor, Adm. Christopher Grady, was not included in high-level White House meetings leading up to the strikes in Yemen on March 15, according to four military officials. And Mr. Hegseth has threatened to administer polygraph tests to suspected leakers, a senior Joint Staff official said.

This month, Gen. Dan Caine, a former fighter pilot Mr. Trump brought out of retirement, took over as the new Joint Chiefs chairman. One of his key tasks will be to convince Mr. Hegseth that he can trust senior officers in the Pentagon and around the world.

Another big challenge for Mr. Hegseth will be learning how to run the Defense Department, the federal government’s largest bureaucracy, while also defending its civilian work force from potentially paralyzing cuts.

Mr. Trump has vowed to ramp military spending up to $1 trillion, a significant rise from the current $850 billion budget. Despite the promised increase in spending from the president, Mr. Musk has not relented from his vow to find tens of billions of dollars in savings in the Defense Department.

Publicly, Mr. Hegseth has welcomed Mr. Musk and his team to the Pentagon and even promoted some of the savings that they have said they have found.

In private, he and Mr. Musk’s team have sparred over cuts to civilians who work in military hospitals, shipyards, munitions factories and schools. A senior official representing Mr. Musk’s effort in the Pentagon was recently replaced because Mr. Musk believed he wasn’t willing to make deep enough cuts, defense officials said. This month, Mr. Musk and Mr. Hegseth met at the White House to try to hash out their differences, according to current and former defense officials.

It wasn’t clear whether the two had come to an agreement.

On Capitol Hill, cracks in G.O.P. support for Mr. Hegseth are appearing.

The defense secretary is under an inspector general review over the disclosure by The Atlantic of a Signal chat in which Mr. Hegseth revealed the flight sequencing for the Yemen strikes.

Roger Wicker, a Mississippi Republican who chairs the Senate Armed Services Committee, and the committee’s senior Democrat, Jack Reed of Rhode Island, requested the review.

News of the second Signal chat, in which Mr. Hegseth shared the same information about the Yemen strikes with his wife and Pentagon officials, prompted Representative Don Bacon of Nebraska to become the first Republican lawmaker to openly suggest that Mr. Hegseth should be fired.

In an interview with Politico on Monday, Mr. Bacon, a former Air Force general, said of Mr. Hegseth’s Signal disclosures: “I find it unacceptable, and I wouldn’t tolerate it if I was in charge.”

Mr. Hegseth was confirmed by a razor-thin, one-vote margin in the Senate and needed the intervention of Vice President JD Vance to break the tie.

Amid the chaos, Mr. Hegseth has sought to model the “warrior ethos” that he says has been missing from too much of the armed forces.

In the past month, he has posted 16 videos and still photos of himself on the social media platform X working out with combat troops around the world.

“Every rep, every drop of sweat, reminds us of the toughness and tenacity that defend our nation,” he wrote last week.

Theodore Schleifer and Eric Schmitt contributed reporting.