In remarks Thursday at the White House, Trump repeated his dislike of Sen. John McCain, a fellow Republican who emerged as a strong critic of the president before his 2018 death. But Trump denied ordering any steps to hide the ship, which is named for McCain’s grandfather and father, both admirals, and the senator from Arizona.

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“Somebody did it because they thought I didn’t like him, okay? And they were well meaning,” he said. “I didn’t know anything about it. I would never have done that.”

Acting defense secretary Patrick Shanahan also denied that he knew about the effort to keep the USS John S. McCain in the background. However, it is not clear who else in Shanahan’s office might have known or whether it was kept from Shanahan, whose nomination must still be confirmed by the Senate.

Speaking to reporters on a trip to Asia, Shanahan said his chief of staff, Eric Chewning, would investigate.

The situation has highlighted a debate about whether Defense Department leaders have permitted the politicization of the military under Trump, who has frequently used military events to deliver campaign-rally-style speeches.

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Remaining out of the fray of partisan politics has long been a central tenet of U.S. military leaders’ philosophy, seen as key to retaining the trust and backing of the American public and maintaining support of politicians who fund them. But since Trump took office, the military has found itself thrust into the political crosshairs, risking an erosion of the traditional civil-military divide as the political climate grows more partisan.

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The Navy’s top officer, Adm. John Richardson, said in an interview with The Washington Post that he was still gathering facts about what happened and promised to cooperate with Shanahan’s investigation.

“It goes without saying” that service members are expected to remain apolitical, Richardson said.

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“Part of this trust and confidence that we have not only up and down the chain of command but also just as importantly with the American people is that we do support and defend the Constitution of the United States,” he said in his office at the Pentagon. “We are apolitical by nature, and so that needs to be maintained.”

If there was direction from the White House on the issue, “it would not be a surprise” if the Navy personnel involved sought to carry it out, Richardson said.

“We are obviously going to take that direction very, very seriously,” he added. “But I really need to understand the sequence of events.”

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While many presidents have used military service members and assets as a backdrop for political remarks, Trump has gone a step further, making overtly political comments to service members and signing “Make America Great Again” campaign hats for troops during a trip to Iraq and Germany last year.

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The messages sent by the commander in chief appear to have made some service members, even if acting on their own, feel emboldened to take certain actions they might have eschewed otherwise. In another moment that drew scrutiny during Trump’s recent trip to Asia, naval aviators were photographed wearing arm patches that appeared to be a riff on his “Make America Great Again” campaign slogan.

The McCain, which suffered a collision that led to the deaths of 10 sailors in 2017, did not receive an invite for its crew to see Trump’s Memorial Day speech and instead was given the day off, according to a Navy official who said the crew of another vessel, the USS Stethem, also did not participate.

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The incident involving the president’s trip, first reported by the Wall Street Journal, has refocused attention on the role Shanahan will play if confirmed as Pentagon chief. The former Boeing executive vowed to retain the military’s apolitical culture upon taking over the job from Defense Secretary Jim Mattis early this year. But he also faces skepticism, even from Republican lawmakers, about whether he will stand up to Trump when necessary.

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Joseph J. Collins, a retired Army colonel and professor at the National Defense University, said on Twitter that White House staffers are not authorized to issue such military directives — unlike the president, they are not in the chain of command.

Collins said senior Pentagon officials should have asked whether the demands about the McCain constituted orders from the president being given through the defense secretary. If not, the officials should have declined to follow them, Collins said.

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If the secretary of defense or the secretary of the Navy did not know about the directive, then they are failing to protect their uniformed personnel from an “imperial” White House staff, Collins added.

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“This is a very bad precedent,” Collins said, referring to Shanahan’s acknowledgment that he did not know about the order.

Kori N. Schake, deputy director general of the International Institute for Strategic Studies and co-editor with Mattis of a book about civil-military relations, said that the incident should raise concern but that it is too early to say where responsibility rests or how serious it is.

Apart from possible chain-of-command issues, Schake said that liaison officers in the White House may have been trying to make a difficult president’s visit go smoothly and Pentagon officials may have been trying to comply — “ending up compromising the professionalism of everyone involved.”

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Schake said it suggests that the Defense Department under Shanahan is allowing a politicization of attitudes.

“That lack of discipline,” Schake said, “will be damaging to the relationship of our military with the public and with political leaders, both of which will begin to view our military as political actors.”

Late Thursday, Trump alluded to a tweet the Navy sent Wednesday night that accurately said the McCain name was not covered up during his visit but left out that it had been a day or two earlier at the request of the White House.