WASHINGTON — 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 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, Hegseth briefly agreed to promote him, only to change course again early this month, the officials said. This time, Hegseth maintained that the senior officer was too close to Gen. Mark Milley, a former chair of the Joint Chiefs of Staff whom President Donald Trump has accused of disloyalty.

Hegseth’s sudden reversal prompted a rare intervention from Gen. Dan Caine, the current chair of the Joint Chiefs. He urged Hegseth to reconsider, said the officials, who spoke on the condition of anonymity to discuss internal deliberations.

Hegseth met with Sims one final time but refused to budge.

Sims is expected to retire in the coming months after 34 years in the military, officials said. Through a spokesperson, Sims and Caine declined to comment. A Pentagon spokesperson declined to comment on Hegseth’s role.

The standoff over his promotion reflects an ongoing clash between Hegseth’s highly partisan worldview, in which he has written that the Democratic Party “really does hate America,” and the long-standing tradition of an apolitical military that pledges an oath to the Constitution.

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.

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.

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 infighting, investigations and personnel churn have strained Hegseth’s ability to manage critical operations in the Pentagon.