The Wall Street Journal first reported last Thursday that the White House wanted the Navy to put "out of sight" the warship initially named after the father and grandfather of the late Republican Senator John McCain while Trump was visiting Japan over Memorial Day weekend.
Trump has frequently criticised the late senator and Navy captain who was held as a prisoner of war in Vietnam - before and after his death.
White House and Pentagon officials told the Washington Post that lower-level staff had been trying to please the President without high-level directives.
The officials, though, confirmed that a member of the White House staff sent a message to military officials in the Pacific asking them to keep the ship out of photos during Trump's visit to the Japanese port of Yokosuka.
Trump himself has offered mixed accounts of what happened. He initially tweeted that he was "not informed about anything having to do with the Navy Ship USS John S. McCain during my recent visit to Japan," though he also repeated his disdain for McCain and suggested those who wanted the ship obscured had good intentions.
"I was not a big fan of John McCain in any shape or form," Trump said. "Now, somebody did it because they thought I didn't like him, OK? And they were well-meaning."
Later, the President seemed to question reporting about the story, tweeting: "The Navy put out a disclaimer on the McCain story. Looks like the story was an exaggeration, or even Fake News - but why not, everything else is!"
That seemed to be a reference to the Navy chief of information tweeting, "The name of USS John S. McCain was not obscured during the POTUS visit to Yokosuka on Memorial Day. The Navy is proud of that ship, its crew, its namesake and its heritage."
The Navy's statement provides official confirmation that a request occurred, though it does not say who made the request of the military. The efforts that were actually taken to obscure the ship or prevent its sailors from participating in an event with the President remain a subject of debate.
The ship's crew was not invited to an event on another ship, the USS Wasp, during Trump's visit, but a Navy official has previously told the Post that was because its crew was released from duty for Memorial Day weekend. So, too, was the crew of a third ship, the USS Stethem, the official said.
There were photographs taken of a tarp obscuring the McCain name on May 24, though a Navy spokesman has said previously it was taken down the following day and the ships remained in "normal configuration" during Trump's visit. The Journal reported that at one point, a barge was moved closer to the USS McCain in such a way that its name was obscured.
