WASHINGTON — The secretary of the Army emphasized the importance of process and deliberation Tuesday when he was asked about President Donald Trump's intervention in controversial cases, two days after the Pentagon forced out Navy Secretary Richard Spencer over his handling of a case involving a SEAL who had been convicted of misconduct.

"Like all things, we have processes that we need to go through," Army Secretary Ryan McCarthy told CNBC as he faces his own potentially tricky matter involving a misconduct case in his ranks and intervention by Trump.

McCarthy's comments come on the heels of Trump's decision to pardon Army Maj. Mathew Golsteyn, who was stripped of his military honors in 2015 after an investigation into combat misconduct.

"What we're trying to really focus on is to go through deliberative processes to make the appropriate-level judgments and get our soldiers through the various transitions," he continued, adding that he didn't have "all the specific details" regarding Spencer's discussions with the White House.

Last year, Trump hinted in a tweet that he may intervene in Golsteyn's case. Last month, he tweeted again about the former Army Green Beret, writing: "We train our boys to be killing machines, then prosecute them when they kill!"

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Since his presidential pardon, Golsteyn has worked to regain his Special Forces tab in a way similar to Navy Chief Petty Officer Edward Gallagher and his quest to retain the Navy SEAL trident pin.

Gallagher, 40, was demoted in rank and pay grade after being convicted by a military jury in July of illegally posing for pictures with the corpse of an ISIS fighter. He was acquitted of premeditated murder for allegedly killing a wounded captive during his 2017 deployment to Iraq.

Last week, Spencer said that Gallagher's membership in the SEAL community should be decided by a board of his peers. Trump had previously said that Gallagher's status must be restored. Spencer had reportedly threatened to quit his post after Trump intervened in the case.

On Sunday evening, the Pentagon said in a statement that Defense Secretary Mark Esper had lost trust and confidence in Spencer and called for his resignation.

Spencer took parting shots at Trump in a letter saying that "the rule of law is what sets the United States apart from its adversaries" and that he and Trump "no longer share the same understanding of the key principles of good order and discipline."

Read more: Pentagon fires Navy Secretary Richard Spencer after controversy over Navy SEAL case

On Monday, Esper offered an explanation of the events leading to Spencer's removal from the Navy's top civilian post and reiterated Trump's authority to address the matter.

As commander in chief, Trump had "every right, authority and privilege to do what he wants to do," Esper said in regard to the handling of Gallagher's case.

Esper also said Monday that Trump ordered the Pentagon to let Gallagher retain his elite Trident pin.

Read more: Trump ordered the Pentagon to let convicted Navy SEAL keep his elite status, Esper says

Trump wrote in a string of tweets Sunday that Spencer was fired over the way the Navy handled Gallagher's case as well as cost overruns that were not addressed to his satisfaction. Ken Braithwaite, a retired rear admiral and currently ambassador to Norway, will be nominated to replace Spencer, Trump wrote.

If confirmed by the Senate, Braithwaite would become the 77th secretary of the Navy.

— Yelena Dzhanova contributed to this report from CNBC's global headquarters in Englewood Cliffs, New Jersey.