The warship is named for the late Arizona senator with whom the president repeatedly and publicly clashed, including by insulting his military service.
In an email setting out instructions for Mr Trump’s weekend visit an official from the US’ Indo-Pacific Command said the destroyer “needs to be out of sight”, the Wall Street Journal reported. The email’s existence was later confirmed by the Associated Press who spoke to three US officials.
The Journal reported that a tarpaulin was placed over the McCain‘s name before Mr Trump arrived, according to photos it reviewed, and that sailors were instructed to remove any coverings from the ship that included its name.
It also reported that sailors from the McCain were given the day off during Mr Trump’s visit. Those who did turn up to watch the president speak – wearing uniforms bearing their ship’s insignia – were asked to leave, according to the New York Times.
McCain’s daughter, Meghan, tweeted in response to the story: “Trump is a child who will always be deeply threatened by the greatness of my dads incredible life.
“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.”
On Thursday Mr Trump 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!”
He did not say that he was not told about the ship beforehand. The Independent has contacted the White House for comment.
The US Navy denied it had covered up the McCain. It said on Twitter: “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.”
Pat Shanahan, the acting defence secretary, said the Journal story was “the first I heard about” the request.
Commander Clay Doss, a spokesman for the US 7th Fleet, said the tarpaulin was on the ship on Friday but had been removed by Saturday morning, when Mr Trump arrived. “All ships remained in normal configuration during the president’s visit,” he said.
Two US officials said that all the ships in the harbour were lined up for Mr Trump’s visit, and they were visible from the USS Wasp aboard which he was due to speak. The officials said, however, that most of their names probably could not be seen since they were side by side but that the McCain‘s name could be seen from the pier.
Officials said the tarpaulin had been placed on the ship for maintenance and removed for the visit. A paint barge was reportedly in front of the destroyer on Saturday morning when 7th Fleet officials walked the pier to see how everything looked for the visit.
It was ordered to be moved and was gone by the time Mr Trump arrived, the officials said.
Sailors from the McCain were not told to stay away but that many were away for the long weekend, officials also said.
They added that some 800 sailors from more than 20 ships and Navy commands were aboard the USS Wasp during the president’s visit, and all wore the same Navy hat that has no logo, rather than wearing individual ship or command hats.
In 2017, 10 sailors died when the McCain collided with a container ship and suffered serious damage.
Additional reporting by AP