President Trump widened a rift with top U.S. military commanders Thursday by publicly ordering the Pentagon to abandon a process that could have resulted in booting Navy SEAL Edward Gallagher out of the elite unit — an unexpected power play by the commander in chief that has left the Navy in what one former senior Pentagon official called a “no-win situation.”

In a Thursday morning tweet, the president declared that Navy officials will not follow through with a review process that likely would have seen Mr. Gallagher stripped of his Trident Pin, which symbolizes membership in the SEALs. Mr. Gallagher was acquitted earlier this year of murder and other charges in connection with the 2017 killing of an Islamic State militant in Iraq.

He was, however, demoted from chief petty officer to petty officer first class and sentenced to four months in jail as punishment for posing for photographs with the militant’s corpse. Military officials say his case is becoming a test of the services’ ability to police their own.

But conservative activists and some veterans groups have decried the continuing action against Mr. Gallagher, noting that he was already planning his retirement and successfully lobbying Mr. Trump to overrule the military court.

“It’s not something that you’re supposed to [do] after somebody put in their papers for retirement so you can kick them on out the way out,” Mr. Gallagher’s attorney, Timothy Parlatore, told USNI News, published by the independent nonprofit U.S. Naval Institute, on Thursday.

Mr. Trump reversed that demotion last Friday and restored Mr. Gallagher’s previous rank in the SEALs, a move the White House said was “justified” because of his service to the nation.

The decision ruffled feathers inside the military, and some top officials believed that Mr. Gallagher must pay a public price for what happened in Iraq in 2017. Just 72 hours after the president restored Mr. Gallagher’s rank — a move made in conjunction with the pardons of two other service members convicted of war crimes, Army Green Beret Maj. Matt Golsteyn and former Army 1st Lt. Clint Lorance — the Navy this week summoned Mr. Gallagher to attend a “peer review” proceeding next month. The peer-review panel ultimately would have decided whether to strip his Trident Pin, effectively kicking him out of the SEALs.

The removal of Mr. Gallagher’s Trident Pin would have undone Mr. Trump’s action last week and would have represented a rare example of new punishment being doled out after presidential intervention in a case.

With one tweet, the president quickly upended the Navy’s strategy.

“The Navy will NOT be taking away Warfighter and Navy Seal Eddie Gallagher’s Trident Pin,” the president said in his Thursday tweet. “This case was handled very badly from the beginning. Get back to business!”

Navy officials offered no official public response to the president’s comments. Given his status as commander in chief, Mr. Trump surely has the authority to stop the review process, though such a move will spark new tensions with military leaders and already has fueled criticism that the president is interfering in matters best handled by career military officers.

National security specialists also say that Mr. Trump has left the Navy with two bad options: Continue on with the review process in defiance of the president, or halt it and face a backlash from critics who believe Mr. Gallagher must be held accountable in some form or fashion.

“The Navy is in a no-win situation over Chief Gallagher,” said J.D. Gordon, a former Pentagon spokesman and national security adviser to Mr. Trump. “If they revoke his Trident like over 150 other SEALs during this decade, it will be seen as a direct rebuke of President Trump. If they don’t, the mainstream media will try to destroy the careers of Navy leaders far higher in the chain of command, from San Diego to the Pentagon.”

Rob Bracknell, a former Marine and military lawyer, told USNI News that Mr. Trump’s repeated interventions in the Gallagher case were “virtually unprecedented,” but added SEAL commanders have been particularly provocative in reacting to Mr. Trump’s orders.

“The SEAL commander should be mindful of picking a public fight with the [president], and the implications it could have for civil-military relations at a particularly strained point in our history,” he said.

But the past week has seen sharp criticism of the administration from critics who allege that Mr. Trump is effectively shielding a convicted war criminal. Navy officials could face similar criticism if they take no further action.

“With this utterly shameful use of presidential powers, Trump has sent a clear message of disrespect for law, morality, the military justice system, and those in the military who abide by the laws of war,” Hina Shamsi, director of the National Security Project at the American Civil Liberties Union, said in response to Mr. Trump’s initial move last week.

The Navy’s peer review proceeding could still go forward, though such a path would appear pointless since Mr. Trump has made clear what the outcome will be.

Thursday’s move is the latest in a series of actions that have strained Mr. Trump’s relations with top military officials.

Most notably, the president’s decision last December to begin a drawdown of American forces in Syria angered Pentagon leaders and led directly to the resignation of then-Defense Secretary James Mattis. His more recent decision to remove U.S. troops from the Syria-Turkey border — allowing a Turkish military attack on U.S.-backed Kurdish fighters in Syria — also was deeply unpopular inside the Defense Department.

Privately, military officials also have been at odds with the president over the deployment of U.S. forces to the Mexican border, the cancellation of military drills with South Korea as part of diplomatic outreach to North Korea, and on a host of other issues.

As for Mr. Gallagher, the president’s Thursday morning Twitter announcement came shortly after Mr. Gallagher’s attorney, Timothy Parlatore, appeared on Fox News and accused the Navy of trying to publicly defy the White House. Mr. Parlatore specifically took aim at Rear Adm. Collin Green, commander of Naval Special Warfare Command.

“Monday morning the admiral comes in and says, ‘I disagree with the president, I’m going to take his Trident,’ ” Mr. Parlatore told the “Fox & Friends” television program, which Mr. Trump is known to watch. “It’s incredible that they still can’t let this go.”

Mr. Gallagher served eight combat tours during his two decades as a Navy SEAL.

There was also grumbling on Twitter about Mr. Trump’s pardon for Mr. Gallagher, along with some dark predictions about how his superiors will treat him following his reinstatement.

In the comment section at Fark.com, many predicted Mr. Gallagher should expect rough treatment.

“The Navy will assign him to the [back] end of a destroyer escort in the North Atlantic and keep him there through a couple of bad reviews, at which point he will be kicked off the [back] end of the boat,” one commenter predicted.

• Rowan Scarborough contributed to this report.

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