The Pentagon has told the White House that the US military will not be politicized, a US official said on Sunday, amid a controversy after officials directed the US Navy to keep the USS John S. McCain out of sight during a recent speech by President Donald Trump in Japan.

The White House military office directed the US Navy's Seventh Fleet to minimize the visibility of the USS John S. McCain, a warship bearing the name of Trump's former political rival, during a speech by the president in Japan last week.

While the directive was not implemented after senior Navy officials found out about the request, the incident has raised questions about the politicization of the military.

"Secretary [Patrick] Shanahan directed his chief of staff to speak with the White House military office and reaffirm his mandate that the Department of Defense will not be politicized," Lieutenant Colonel Joe Buccino, a Pentagon spokesman, said in a statement.

"The chief of staff reported that he did reinforce this message."

Concern has increased about the politicization of the US military under Trump. He has given a number of overtly political speeches to military audiences and the military has been drawn into a mission along the border with Mexico, which some critics have described as a political stunt rather than a national security necessity.