WASHINGTON — President Trump doubled down on Monday on his decision to intervene in several high-profile war crimes cases, comparing his leniency for a handful of American service members with actions taken by President Barack Obama, which Mr. Trump said were far worse.
Under fire over his insistence that a Navy SEAL convicted of misconduct not be punished, Mr. Trump sought to defend actions that have roiled the Pentagon, angered senior military leadership and led to the firing of the Navy secretary. Mr. Trump said that his refusal to allow the Navy to oust Chief Petty Officer Edward Gallagher from the SEALs showed he was sticking up for “warriors,” and not traitors.
“You have a Chelsea Manning, who stole classified information and did many, many things that were not good and gets pardoned or whatever happened,” Mr. Trump told reporters at the White House.
He was referring to the former Army intelligence analyst who disclosed a trove of military and diplomatic documents to WikiLeaks. Ms. Manning spent nearly seven years in a military prison before Mr. Obama commuted her sentence; she was not pardoned.
And Bowe Bergdahl, an Army sergeant who walked off his base in Afghanistan and was convicted of desertion but received no jail time, was cited by Mr. Trump to defend his actions. Mr. Bergdahl, Mr. Trump said, received “a slap on the wrist, and they want to put these warriors in jail for 25 years.”
Mr. Bergdahl spent five years as a hostage of the Taliban before he was released in a prisoner swap. His court-martial resulted in a dishonorable discharge and reduction in rank.
Mr. Trump’s comparison of his intervention in the case of Chief Gallagher with the two previous cases echoed talking points frequently used by the president’s conservative base and by hosts on Fox News, his preferred news outlet.
The Pentagon on Monday continued reeling from the fast-moving events of this past weekend, which culminated in the firing of the Navy secretary, Richard V. Spencer. Defense Secretary Mark T. Esper repeated the convoluted story that he put out on Sunday in which Mr. Spencer was negotiating a deal for Chief Gallagher with the White House in private, while publicly telling people, including Mr. Esper, that he supported a process that would punish Chief Gallagher. The Navy secretary, Mr. Esper said, even threatened to resign rather than follow Mr. Trump’s wishes that Chief Gallagher not be punished.
“He certainly indicated he was probably going to resign,” Mr. Esper told reporters at the Pentagon.
He said that Mr. Trump had issued a formal order that Chief Gallagher’s Trident pin, indicating his membership in the elite Navy commando unit, not be removed, and that the Defense Department would adhere to it.
Mr. Spencer spoke with CBS News and warned of the message being sent to the troops. Now that the Pentagon has called off the review into Chief Gallagher’s status as a SEAL, Mr. Spencer said that it meant that “you can get away with things.”
“We have to have good order and discipline,” Mr. Spencer told CBS. “It’s the backbone of what we do.”
A senior Democratic national security expert in the Senate agreed that the damage to the ideal that American troops adhere to a strict code of justice and ethics would be around for a long time.
“This was an outrageous, irresponsible interference by President Trump in the military justice system,” Senator Jack Reed, Democrat of Rhode Island and an Army veteran, said in a statement. “It signals to people that they can operate outside the rule of law and the Geneva Convention.”
Chief Gallagher was accused of shooting civilians, killing a captive Islamic State fighter with a hunting knife in Iraq and threatening to kill SEALs who reported him, among other misconduct. His court-martial ended in acquittal on those charges, but he was convicted of one charge of bringing discredit to the armed forces by posing for photographs with the teenage captive’s body.
The Navy demoted him, but Mr. Trump reversed that decision this month, angering Navy officials, including the commander of the SEALs, Rear Adm. Collin Green, and Mr. Spencer. When Mr. Spencer and Admiral Green indicated they were moving ahead with plans to strip Chief Gallagher of his Trident pin, Mr. Trump was angered, and that set off this past week’s chain of events.
Administration officials said that Mr. Esper and Gen. Mark A. Milley, the chairman of the Joint Chiefs of Staff, learned of Mr. Spencer’s secret proposal to the White House on Friday, outside the Oval Office, as the two men were preparing to meet with the president. Pat A. Cipollone, the White House counsel whose office has been involved in Mr. Gallagher’s case, gave them the news, the officials said. Mr. Spencer had discussed the proposal — that if the White House remained out of it, he could guarantee the outcome — with him at some point before Friday.
“Chairman Milley and I were caught completely off guard,” Mr. Esper said.
Mr. Esper said he spoke to Mr. Spencer, who confirmed he had a discussion with the White House counsel’s office. Mr. Esper then called the president on Saturday and said he had lost confidence in Mr. Spencer. Mr. Trump was also surprised to see reports on Sunday that a Navy official said the White House would not be interfering in the review process, according to two administration officials.
Also Saturday, a White House official contacted Mr. Spencer seeking clarity on whether he had threatened to resign, suggesting it was on the president’s mind as he made his decision.
Officials insisted that Mr. Trump had been unhappy with Mr. Spencer for at least two months, including over budget and weapons matters.
In the past two weeks, Mr. Trump told the national security adviser and Secretary of State Mike Pompeo that it was time to fire Mr. Spencer, officials said; as he had before, he cited what he saw as mismanagement of the Navy and, in particular, cost overruns related to the Gerald R. Ford aircraft carrier. Officials noted that Mr. Spencer said in January that Mr. Trump should “fire me” if it was not fixed by summer.
So when Mr. Esper called Mr. Trump, they found they were in agreement on Mr. Spencer’s status, officials said. Mr. Trump told advisers he would adhere to the chain of command and let Mr. Esper go ahead with the actual dismissal.
Mick Mulvaney, the acting White House chief of staff, said of Mr. Spencer, “The president was very concerned about his overall performance.”
In a letter acknowledging his termination on Sunday, Mr. Spencer said that he regarded good order and discipline throughout the Navy’s ranks to be “deadly serious business.”
He added: “Unfortunately, it has become apparent that in this respect, I no longer share the same understanding with the commander in chief who appointed me, in regards to the key principle of good order and discipline. I cannot in good conscience obey an order that I believe violates the sacred oath I took.”
Former administration officials expressed surprise that Mr. Spencer had survived as long as he had, partly because he was seen as part of a group of people who came in under Defense Secretary Jim Mattis when he was still in favor with Mr. Trump. Mr. Mattis resigned over administration policy.
“My views on treating allies with respect and also being cleareyed about both malign actors and strategic competitors are strongly held,” Mr. Mattis wrote. “Because you have the right to have a secretary of defense whose views are better aligned with yours on these and other subjects, I believe it is right for me to step down from my position.”