The US navy secretary said on Saturday he did not threaten to resign amid a disagreement with Donald Trump over whether a Navy Seal convicted of battlefield misconduct should face a board of peers who may oust him from the elite force.

“Contrary to popular belief, I’m still here,” Richard V Spencer said at a security conference in Halifax, Canada. “I did not threaten to resign. But let us just say we are here to talk about external threats, and Eddie Gallagher is not one of them.”

The New York Times reported earlier that Spencer and Rear Adm Collin Green threatened to quit if the president subverted the process.

In July, a military jury convicted Edward Gallagher, special operations chief, of illegally posing for pictures with the corpse of an Islamic State fighter, but acquitted him of murder in the detainee’s death. Gallagher also was cleared of charges that he deliberately fired on unarmed civilians.

Spared a prison sentence, he was demoted in rank and pay grade for his conviction, which stemmed from a 2017 deployment in Iraq.

Last week, Trump intervened in the case, ordering the navy to restore Gallagher’s rank and pay, clearing the way for him to retire on a full pension.

But on Tuesday the navy notified Gallagher, 40, that a five-member panel of fellow commandos would convene on 2 December to review his case and recommend whether he is fit to remain in the Seals.

On Thursday, Trump lashed out, declaring on Twitter: “The Navy will NOT be taking away Warfighter and Navy Seal Eddie Gallagher’s Trident Pin. This case was handled very badly from the beginning. Get back to business!”

But the decision as to whether Gallagher will lose his special warfare trident pin ultimately rests with the navy’s personnel command in Washington.

On Friday, Reuters reported that Spencer said Gallagher should face a board of his peers because “the process matters for good order and discipline”.

On Saturday, Spencer said “good order and discipline is also obeying orders from the president of the United States”, and said he hopes “to contribute going forward”.