LOS ANGELES — The federal Transportation Department on Thursday fulfilled its promise to cancel a nearly $1 billion grant that would have helped pay for California’s bullet train, in yet another blow for the ambitious high-speed rail project meant to connect Los Angeles to the Bay Area.

In a letter to state officials, the Federal Railroad Administration said it had made a final decision to terminate a longstanding agreement to send $928.6 million to the California High-Speed Rail Authority for the first phase of the project, in the Central Valley.

The administration had first said that it planned to cancel the money, and would try to claw back $2.5 billion it had already spent on the high-speed rail network, in February, after Gov. Gavin Newsom announced plans to scale back the project.

Federal officials said in the letter Thursday that California “has repeatedly failed to comply” with the terms of the original 2010 agreement “and has failed to make reasonable progress on the project.”