United States Defense Secretary Mark Esper fired the US Navy's top civilian on Sunday over his handling of the case of a Navy SEAL who was convicted of battlefield misconduct in Iraq but later won the support of President Donald Trump.

Navy Secretary Richard Spencer had been pushing for Special Operations Chief Edward Gallagher to face a peer review board that could have led to him being forced out of the elite force.

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The SEAL was acquitted by a military jury in July of murdering a captured and wounded Islamic State of Iraq and the Levant (ISIL or ISIS) fighter in Iraq by stabbing him in the neck, but it convicted him of illegally posing with the detainee's corpse.

That had led to him being demoted.

Trump who had intervened in Gallagher's case to restore his rank cheered the moves.

"Eddie will retire peacefully with all of the honors that he has earned, including his Trident Pin," Trump said on Twitter.

Esper determined that Gallagher should also be allowed to retain the so-called Trident pin that designates him a SEAL, effectively ending the Navy's efforts to carry out the review.

'Good order and discipline'

The White House said in November that Trump had restored Gallagher's rank and had pardoned two Army officers accused of war crimes in Afghanistan.

Critics said such actions would undermine military justice and send a message that battlefield atrocities would be tolerated.

I was not pleased with the way that Navy Seal Eddie Gallagher’s trial was handled by the Navy. He was treated very badly but, despite this, was completely exonerated on all major charges. I then restored Eddie’s rank. Likewise, large cost overruns from past administration’s.....

— Donald J. Trump (@realDonaldTrump) November 24, 2019

In a letter published in media reports, Spencer took parting shots at Trump and defended the need to preserve "good order and discipline throughout the ranks" - something Navy officials had believed the peer review board would help ensure.

"The rule of law is what sets us apart from our adversaries," Spencer wrote, according to the reports.

"Unfortunately it has become apparent that in this respect, I no longer share the same understanding with the Commander in Chief who appointed me."

The Pentagon declined to immediately provide a copy of Spencer's letter.

However, Pentagon spokesman Jonathan Hoffman offered a different version of events leading up to Spencer's dismissal, saying Spencer also had a private line of communications with the White House.

"Secretary Spencer had previously and privately proposed to the White House - contrary to Spencer's public position - to restore Gallagher's rank and allow him to retire with his Trident pin," Hoffman said.

Spencer never informed Esper of his private proposal, Hoffman said.

Esper decided to ask for Spencer's resignation after "losing trust and confidence in him regarding his lack of candour over conversations with the White House," Hoffman said.

Esper had favoured letting the review process "play itself out objectively and deliberately, in fairness to all parties," Hoffman said. But that now appeared impossible.

"At this point, given the events of the last few days, Secretary Esper has directed that Gallagher retain his Trident pin," Hoffman said.