In a tweet on Wednesday night, Trump denied having any information about the request after a report by The Wall Street Journal, later confirmed by The Associated Press, that a White House email to military officials had requested that it "move out of sight" during the president's visit to the U.S. Naval base in Yokosuka, Japan, on Monday.
"There was a lower level effort to comply with the request but when leadership became aware they ordered the tarp be taken down," a U.S. Navy official acknowledged to ABC News. "Navy leadership decided the name should not be obscured."
Another U.S. official said there had been "an initial discussion about veiling the ship’s name, but senior Navy leadership directed all ships to be in the normal configuration." The Wall Street Journal reported that the message to cover the ship's name originated with the White House Military Office.
The Navy’s top spokesman, Adm. Charlie Brown, tweeted that the ship’s name had not been obscured.
"The name of USS John S. McCain was not obscured during the POTUS visit to Yokosuka on Memorial Day," Brown tweeted. "The Navy is proud of that ship, its crew, its namesake and its heritage."
The USS John S. McCain has been in service 1994 and was originally named to honor late Arizona Sen. John McCain’s grandfather and father, who were both noteworthy admirals. In July 2018 a month before the senator's death, Navy Secretary Richard Spencer ordered that the ship's name would also honor Sen. McCain.
Officials acknowledged that on Friday a tarp had been placed on the destroyer's stern where the ship's name is located, but that it was ordered removed the following day by base commanders who had decided that all the Navy ships in Yokosuka should adhere to Navy regulations. Trump visited the base on Monday and gave a speech to sailors aboard the USS Wasp, a large amphibious assault ship.
"All ships remained in normal configuration during the President's visit," said Cmdr. Clay Doss, a spokesman for the Navy's Seventh Fleet.
A U.S. official told ABC News that a tarp seen in a photo included in the Journal report had been placed on the ship's stern as part of "hull maintenance and preservation." A Navy official explained that a barge seen in the photo was not there to obstruct the destroyer's name, but is always alongside it to remove its wastewater.
The destroyer has been undergoing a massive repair effort at the base in Japan following a deadly collision in August 2017 in the harbor in Singapore that killed 10 sailors.
The Wall Street Journal report drew outrage from Meghan McCain, the daughter of the late Sen. John McCain, who has been a frequent political foe of Trump.
"Trump is a child who will always be deeply threatened by the greatness of my dads incredible life," McCain tweeted. "There is a lot of criticism of how much I speak about my dad, but nine months since he passed, Trump won't let him RIP. So I have to stand up for him. It makes my grief unbearable."
Trump later tweeted, "I was not informed about anything having to do with the Navy Ship USS John S. McCain during my recent visit to Japan. Nevertheless, @FLOTUS and I loved being with our great Military Men and Women - what a spectacular job they do!"
A spokesman for acting Defense Secretary Patrick Shanahan denied that he was aware of the White House directive.
"Secretary Shanahan was not aware of the directive to move the USS John S McCain nor was he aware of the concern precipitating the directive," said Lt. Col. Joe Buccino, Shanahan's spokesman.
Shanahan is currently in Singapore, where he was asked overnight in the U.S. whether the ship's name was covered or moved.
He said he never "authorized or approved any action of movement or activity regarding the ship" and he would "never dishonor the memory of Sen. McCain, nor disrespect the young men and women that crew the ship.”
While visiting Yokosuka on Monday, Trump spoke to sailors aboard the USS Wasp.
According to a Navy official, ahead of the president's visit all Navy personnel on the base were given 96 hours leave -- not just the McCain’s crew, as reported by The Wall Street Journal.
While sailors typically wear ball caps with their ship's name as part of their uniform, they were not authorized to be worn during the president's speech as a practical matter, according to the official. Because there were sailors from various ships aboard the USS Wasp for the president's remarks the official said that to maintain uniformity all sailors were required to wear their 8-point service covers.
The McCain's crew was not told to avoid the event, said the official.