In the spring, Defense Secretary Pete Hegseth decided not to promote a senior Army officer who had led troops over five tours in Afghanistan and Iraq because Mr. Hegseth suspected, without evidence, that the officer had leaked sensitive information to the news media, according to three people with knowledge of the matter.
When Lt. Gen. Douglas A. Sims II was cleared of the allegations, Mr. Hegseth briefly agreed to promote him, only to change course again early this month, the officials said. This time, Mr. Hegseth maintained that the senior officer was too close to Gen. Mark Milley, a former chairman of the Joint Chiefs of Staff whom President Trump has accused of disloyalty.
Mr. Hegseth’s sudden reversal prompted a rare intervention from Gen. Dan Caine, the current chairman of the Joint Chiefs. He urged Mr. Hegseth to reconsider, said the officials, who spoke on the condition of anonymity to discuss internal deliberations.
Mr. Hegseth met with General Sims one final time but refused to budge. General Sims is expected to retire in the coming months after 34 years in the military, officials said. Through a spokesman, General Sims and General Caine declined to comment. A Pentagon spokesman declined to comment on Mr. Hegseth’s role.
The standoff over his promotion reflects an ongoing clash between Mr. Hegseth’s highly partisan worldview, in which he has written that the Democratic Party “really does hate America,” and the longstanding tradition of an apolitical military that pledges an oath to the Constitution.
Mr. Hegseth’s actions could shape the military’s top ranks for years to come. His insistence on absolute loyalty, backed with repeated threats of polygraphs, also creates uncertainty and mistrust that threaten to undermine the readiness and effectiveness of the force, officials said.
The tension between top military officers and their civilian leaders has been persistent since the earliest days of Mr. Trump’s second term, when senior administration officials ordered the removal of General Milley’s portrait from a Pentagon hallway.
General Caine, who pressed Mr. Hegseth on General Sims’s behalf, got the job of Joint Chiefs chairman after Mr. Hegseth and President Trump fired Gen. Charles Q. Brown Jr., his predecessor. Mr. Hegseth accused General Brown, who is Black, of prioritizing diversity over the combat effectiveness of the force.
Also removed during the first months of the new administration were the first woman to command the Navy, Adm. Lisa Franchetti; the first woman to command the Coast Guard, Adm. Linda Fagan; Mr. Hegseth’s senior military assistant, Lt. Gen. Jennifer Short; and the U.S. military representative to the NATO military committee, Vice Adm. Shoshana Chatfield. All were dismissed as part of a campaign to root out diversity, equity and inclusion from the military and restore what Mr. Hegseth has described as a “warrior ethos.”
Mr. Hegseth also recently withdrew the nomination of Rear Adm. Michael “Buzz” Donnelly to lead the Navy’s Seventh Fleet in Japan — its largest overseas force — amid reports in conservative media that seven years earlier the admiral had allowed a drag performance to take place on the aircraft carrier Ronald Reagan.
The decision not to promote General Sims, who is white, seems unrelated to any issues of race or gender. Rather, the general’s career seems to have become tangled up in broader suspicions about leaks and a mistrust of senior military officers that have defined much of Mr. Hegseth’s first six months on the job.
Mr. Hegseth, a former Fox News host and an Iraq war veteran, came to the Pentagon with little managerial experience. Since his arrival, a series of firings and resignations in his inner circle have left him with only a skeleton staff of civilian aides to run his office. He has been without a permanent chief of staff since late April. Ricky Buria, a recently retired Marine colonel who has forged a close relationship with Mr. Hegseth, has been serving in the critical role.
But White House officials, who have concerns about Mr. Buria’s competence and qualifications, have blocked Mr. Hegseth from formally appointing him to the job, officials said. Mr. Buria, meanwhile, has clashed repeatedly with many of Mr. Hegseth’s closest aides and some officers in the Pentagon.
This spring, Eric Geressy, a retired sergeant major who served with Mr. Hegseth in Iraq and now advises him in the Pentagon, threatened to quit after an argument with Mr. Buria, according to people with knowledge of the situation. The rift was reported earlier by The Washington Post. Mr. Geressy briefly went to his home in Florida before Mr. Hegseth persuaded him to return, officials said.
Mr. Hegseth is also still contending with a review by the Pentagon’s inspector general related to his disclosure on the Signal messaging app of the precise timing of U.S. fighter jets’ airstrikes against the Iranian-backed Houthi militia in Yemen in March.
The office has received evidence that the information that Mr. Hegseth put in the commercial chat app came from a classified Central Command document, according to two U.S. officials with knowledge of the review. The classified origins of the information were reported earlier by The Washington Post.
The infighting, investigations and personnel churn have strained Mr. Hegseth’s ability to manage critical operations in the Pentagon. Mr. Hegseth found himself in the cross hairs earlier this month after Democrats and Republicans in Congress blamed him for pausing critical shipments of interceptors and other arms to Ukraine without sufficiently consulting with the White House or the State Department.
The suspension was particularly jarring because just days earlier Mr. Trump had said he was open to selling more weapons to Ukraine after meeting with President Volodymyr Zelensky on the sidelines of a NATO meeting in The Hague.
It also left the impression that Mr. Hegseth and his top aides had failed to keep the president and senior White House officials in the loop.
As aides to Mr. Hegseth traded blame, and then tried to play down the impact of the pause, Mr. Trump dramatically overruled the Pentagon, saying he was unhappy with President Vladimir V. Putin of Russia.
In a further twist, Mr. Trump endorsed a plan for NATO countries to send Patriot antimissile systems to Ukraine and replace them by purchasing new arms from the United States. It was an approach conceived by NATO countries. Mr. Hegseth has delegated responsibility for working out details of the arms transfers to senior U.S. military officers in Europe.
The frustration with Mr. Hegseth is seeping out. Senator Thom Tillis, the North Carolina Republican who cast the deciding vote to confirm Mr. Hegseth, this month called him ill-suited to lead the Pentagon.
“With the passing of time, I think it’s clear he’s out of his depth as a manager of a large, complex organization,” Mr. Tillis told CNN.
For now, Mr. Hegseth’s missteps do not seem to have hurt his standing with the person who matters most: Mr. Trump.
Like Mr. Trump, Mr. Hegseth had a career in television before joining the administration and relishes the performative aspects of his job. As defense secretary, he regularly posts videos that show him exercising with troops. The photo ops — known inside the Pentagon as “troop touches” — are a central part of almost all his public appearances, current and former aides said.
Several officials have complained that the photos and videos — including one that he posted from Omaha Beach in Normandy in which he joins Army Rangers carrying a soldier on a stretcher as part of D-Day remembrances — are distractions that serve primarily to bolster his image.
Anna Kelly, a White House spokeswoman, said that Mr. Hegseth retained Mr. Trump’s “full confidence” and cited the “critical role” he played “in ensuring the flawless execution” of the strikes on Iranian nuclear facilities in June.
Current and former military officials said that Mr. Trump largely bypassed Mr. Hegseth in the days leading up to the strikes and instead relied on General Caine and Gen. Michael Erik Kurilla, the head of Central Command, for counsel.
But officials with knowledge of the president’s thinking said that Mr. Trump especially admired his defense secretary’s combative response at a news conference to reports questioning the effectiveness of the attack.
Today Mr. Hegseth is managing the Pentagon with a smaller immediate staff than when he started in January. Several top aides were forced out or quit. In late April, three top aides were fired and escorted from the building. Mr. Hegseth has repeatedly accused them, without offering evidence, of leaking classified information to the media.
The fired aides, who have not been charged with any wrongdoing, were recently told that an investigation into the allegations against them was in its final stages and would soon be shared with the Pentagon’s senior leaders, officials said.
In the wake of their dismissal and a series of negative stories about Mr. Hegseth’s performance in the job, Karoline Leavitt, the White House press secretary, offered a window into how Mr. Hegseth views the department he now runs.
“This is what happens when the entire Pentagon is working against you and working against the monumental change you are trying to implement,” she said.
That same spirit seems to animate the Pentagon today. Only a few months ago, General Sims’s promotion to four stars seemed to be a given. Of the last 21 officers to hold his current position, 19 were promoted to four-star rank.
“He’s the type of person you would want your kids serving under — extremely dedicated, selfless and loyal,” said Brynt Parmeter, who stepped down in June as the Pentagon’s chief talent management officer and has known General Sims for more than three decades.
The Pentagon gave a more muted assessment. In a statement, Sean Parnell, the Pentagon’s chief spokesman, thanked General Sims for his “decades of service.”
“We wish him well in his future endeavors,” Mr. Parnell wrote.
Maggie Haberman contributed reporting.