Defense Secretary Mark Esper ordered the resignation U.S. Navy Chief Richard Spencer on Sunday after a long dispute between the Trump administration and military officials who disagreed on the handling of a war crime case.

In a statement, Esper said he was “deeply troubled” by Spencer’s conduct and that what he was saying in private contradicted his public statements.

Spencer had angered President Donald Trump after he threatened to resign if Trump went through with pardoning Chief Petty Officer Edward Gallagher, whose rank was reduced after he posed for a photo with a corpse. Trump reversed Gallagher’s demotion and pardoned two other military officials on Nov. 15.

Despite Spencer’s public opposition to Gallagher’s pardoning, he had been privately trying to cut a side deal with the White House to let him remain in the elite unit.

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In his letter of resignation dated Sunday, Spencer expressed his frustration about how much control the White House insisted on having over military affairs.

“The lives of our sailors, Marines and civilian teammates quite literally depend on the professional execution of our many missions, and they also depend on the ongoing faith and support of the people we serve and the allies we serve alongside,” he wrote in the letter.

He continued, “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.”

Esper ordered that Gallagher keeps both his rank and trident pin, at the direction of the President.

Esper said, “The president is the commander in chief, he has every right, authority, and privilege to do what he wants to do,” according to tweets from Breaking Defense journalist Paul McLeary.

“If folks want to criticize anyone at this point for reaching down into administrative processes, simply blame me,” he added. “I’m responsible at this point. It’s not where I prefer to be but I’ll own it.”

Trump weighed in on Twitter Sunday, saying he was “not pleased” with how the Navy handled the Gallagher trial and that he had asked for Spencer’s resignation because of this. He added that he will nominate Admiral and Ambassador to Norway Ken Braithwaite to replace Spencer.

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