President Trump has directed the Pentagon to remove thousands of U.S. troops from Germany by September, U.S. government officials said Friday.

The move would reduce the U.S. troop presence in Germany by 9,500 troops from the 34,500 troops that are permanently assigned there.

The move also caps the number of U.S. service members who are in Germany at any one time at the 25,000-troop level. Under current practice, overall troop levels can rise to as high as 52,000 as units rotate in and out or take part in training exercises.

The change was ordered by the White House in a memorandum signed recently by White House National Security Advisor Robert O’Brien, the officials said Friday.

One person familiar with the decision said that it has been under discussion within the administration since September and not linked to the decision by German Chancellor Angela Merkel not to attend a G-7 meeting that Mr. Trump was to host in Washington at the end of June.

But it comes amid sharp strains in U.S. relations with Germany, including over Germany’s level of military spending.

Richard Grenell, the former ambassador to Germany who recently stepped down as the acting director of national intelligence, has long pressed for a troop cut amid complaints that the German government isn’t spending enough on its own defense.

Germany’s defense minister promised last year to meet the NATO goal of spending 2% of its GDP on defense, but the target date for meeting that objective is 2031.

Pentagon officials declined to comment.

Write to Michael R. Gordon at michael.gordon@wsj.com and Gordon Lubold at Gordon.Lubold@wsj.com