WASHINGTON—The Trump administration said Tuesday it would cancel almost $1 billion in funding for the California high-speed rail network, casting doubt on whether the state will be able to complete even the first phase of the troubled project.

In a letter to state officials, Federal Railroad Administrator Ronald Batory said the administration is planning to revoke its grant agreement with the California High-Speed Rail Authority, and halt $928.6 million in future grant payments it was expected to make to fund the project through 2022.

The FRA is also considering a legal effort to recover $2.5 billion in federal funds already spent on the project, which was originally set to link Los Angeles and San Francisco.

California Gov. Gavin Newsomsaid last week that the state would focus on completing the first phase of the project, connecting the cities of Bakersfield and Merced, and revisit plans to extend the network south to Los Angeles and north to San Francisco.

“And by the way, I am not interested in sending $3.5 billion in federal funding that was allocated to this project back to Donald Trump,” Mr. Newsom, a Democrat, said in his State of the State speech.