Navy secretary Richard Spencer has been fired over his handling of the case of Edward Gallagher demoted for misconduct.
The case of the Navy SEAL, who was convicted for posing with a corpse, had sparked tensions between President Donald Trump and military officials.
Edward Gallagher had been due to face a disciplinary review where he could have been stripped of his Seals membership.
There have been differing accounts as to why Richard Spencer was asked to resign.
Defense Secretary Mark Esper said he had lost confidence in Richard Spencer because his private conversations with the White House contradicted his public position.
However, President Trump said he was not happy with “cost overruns” and how Chief Petty Officer Gallagher’s trial was run, and suggested this was why Richard Spencer was fired.
Meanwhile, in a strongly worded letter, Richard Spencer said it was apparent that he and President Trump did not have the same view of “good order and discipline”.
He said: “The lives of our Sailors, Marines and civilian teammates quite literally depend on the professional execution of our many missions.”
President Trump has drawn criticism from parts of the military after pardoning army officers convicted of war crimes.
Edward Gallagher was accused of stabbing an unarmed 17-year-old Islamic State prisoner to death and randomly shooting civilians while serving in Iraq in 2017.
He was acquitted of those charges and convicted only of the lesser charge of posing with the ISIS prisoner’s corpse.
For that, he was demoted, but President Trump later reinstated his rank.
Edward Gallagher was formally notified by navy leaders last week that he would face a disciplinary review which could result in his being stripped of his membership of the Seals.
On November 21, President Trump tweeted his disapproval, saying the navy would “NOT be taking away Warfighter and Navy SEAL Eddie Gallagher’s Trident Pin”.
On November 24, the defense department said Mark Esper had asked Richard Spencer to resign due to “his lack of candor”.
Richard Spencer had made private proposals to the White House, which he did not share with Mark Esper, and had contradicted his public position, Pentagon spokesman Jonathan Hoffmann said in a statement.