The Trump administration carried out its threat to cancel nearly $1 billion in funding for California’s troubled high-speed rail project after Gov. Gavin Newsom said he would scale back its scope.

In a letter Thursday to the head of the California High Speed Rail Authority, Federal Railroad Administrator Ronald Batory confirmed the move the administration had floated in February, officially terminating the Transportation Department’s agreement to provide an additional $928.6 million to help pay for the project.

“It...