Patrick M. Shanahan this weekend admonished the White House to keep politics out of the military amid a furor over efforts to hide the USS John S. McCain from President Trump on Memorial Day — and the clash couldn’t have come at a more crucial, pressure-packed moment for the acting defense secretary.

Mr. Shanahan delivered the blunt message to the president while traveling in Asia, where he gave his first major foreign speech at a high-level security conference in Singapore.

His appearance at the annual Shangri-La forum was a key test of his international gravitas, and Mr. Shanahan used the opportunity to publicly call out China and declare that the U.S. will stand firmly against Beijing’s claim of near-total authority over the vital South China Sea.

But looming over the trip is Mr. Shanahan’s status. Despite a public announcement last month, the White House has yet to follow through and formally nominate the acting secretary to become permanent Pentagon chief. It’s unclear whether his suddenly public political battle with the administration over the USS McCain could undermine Mr. Shanahan’s prospects or change Mr. Trump’s mind about the nomination.

What is clear is that there’s a disconnect between how the White House and Pentagon view the flap over the USS McCain. Top administration officials on Sunday downplayed the incident and even said getting the ship out of Mr. Trump’s line of sight was not an “unreasonable” idea.

Mr. Shanahan, however, has seemed personally offended that such an idea was entertained at all. He reiterated that he had no knowledge of exchanges between White House and naval officials over whether to hide the ship or obscure its name so as not to disturb the president. The ship is named partly after the late Sen. John McCain, a longtime Trump adversary.

Mr. Shanahan’s spokesman, Army Lt. Col. Joseph Buccino, told reporters Sunday that the acting secretary’s chief of staff spoke with top officials in the White House military office over the weekend to “reaffirm his mandate that the Department of Defense will not be politicized.”

Mr. Shanahan also seemed frustrated that naval officials didn’t immediately dismiss the request. He said he was still gathering information and may issue formal guidance to ensure no future controversies.

“How did the people receiving the information? How did they treat it?” Mr. Shanahan said. “That would give me an understanding on the next steps.”

Despite the White House’s steady communication with the Navy, Mr. Shanahan said, little effort was made to hide the USS McCain from Mr. Trump’s line of sight.

The Navy did not move the ship, and a barge that had been in front of it was gone by the time the president arrived in Japan, Mr. Shanahan said. He added that a tarp had been placed over the name of the ship for maintenance reasons but was gone when Mr. Trump showed up.

Although the issue suddenly has become a top priority for Mr. Shanahan, it seems to be a footnote for the White House.

Speaking on “Fox News Sunday,” acting White House Chief of Staff Mick Mulvaney blamed the media for blowing the incident out of proportion.

“The president didn’t know about it. I didn’t know about it,” Mr. Mulvaney said. “We think it’s much ado about nothing.”

Pressed on the disconnect between the White House and the Defense Department, Mr. Mulvaney suggested that a conversation about whether to hide the ship was appropriate given the long-standing feud between Mr. Trump and McCain, who died in August.

“If a 23- or -24-year-old [working in the White House] says, ‘Look, is it really a good idea for this ship to be in the background?’ That is not an unreasonable question to have,” Mr. Mulvaney said. “And it’s certainly not something that takes up two minutes of national television on Sunday.”

The White House reportedly coordinated directly with the Navy’s 7th Fleet about potentially moving the ship, suggesting a much higher-level discussion than either side has acknowledged.

After The Wall Street Journal first broke the story last week, Mr. Trump said administration staffers were “well meaning” but that moving the ship would not have been appropriate. He also reiterated his feelings about the late senator.

“I was not a big fan of John McCain in any way, shape or form,” the president said.

Meanwhile, Mr. Shanahan has had to juggle the McCain controversy with the most important trip of his short career at the Defense Department.

Elevated to acting defense chief on Jan. 1 after the sudden resignation of Defense Secretary James N. Mattis, Mr. Shanahan has spent the past five months working to shore up support inside the Pentagon and on Capitol Hill.

His appearance this weekend at the Shangri-La forum was an important moment for the former Boeing executive, who for the first time had to confront America’s leading geopolitical and economic rival, China, on the world stage. Mr. Shanahan pulled no punches in laying out a U.S. vision for the Indo-Pacific region that centers on pushing back against Chinese aggression.

“Some seem to want a future where power determines place and debt determines destiny, where nations are unable to make use of natural resources within their exclusive economic zones,” Mr. Shanahan said, “where coral reefs are dredged with disastrous ecological and economic consequences, where fishermen’s livelihoods are imperiled as they are denied access to waters they and their ancestors have fished for generations, where freedom of navigation and international overflight are restricted and where the fundamental respect for all people is ignored and religious freedoms are suppressed.

“We can’t wish away reality or continue to look away when countries use friendly rhetoric to distract from unfriendly acts,” he said. “Now is the time to call out the mismatch between words and deeds.”

Chinese Defense Minister Gen. Wei Fenghe delivered a combative response over the weekend, pushing back against the U.S. and saying Beijing’s encroachment throughout the South China Sea represents “the legitimate rights of a sovereign state to carry out construction in its own territory.”

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