The Trump administration said Tuesday that it’s canceling $929 million of federal funding for California’s high-speed rail project and demanding the return of $2.6 billion that’s already been spent.

Gov. Gavin Newsom quickly denounced the move as political retribution for the state’s resistance to a southern border wall and said California will fight for the money.

The administration made its move a week after Newsom suggested that the state was refocusing its $77 billion plan to run 220-mph trains between Los Angeles and San Francisco. Because of cost overruns and delays, he said, the state would concentrate on starting service in the Central Valley between Merced and Bakersfield.

President Trump seized on the governor’s statement in a tweet, calling California’s rail plan a “disaster” and saying he wanted the state to return federal money that has been invested in the project. House Minority Leader Kevin McCarthy, a Bakersfield Republican and close Trump ally who has long opposed the high-speed rail project, also celebrated its “extinction.”

In a letter sent Tuesday to the California High-Speed Rail Authority, Ronald Batory, head of the Federal Railroad Administration, noted Newsom’s “significant retreat” from the state’s original plan. He wrote that the reduced project wasn’t what the federal government had committed to help fund.

The letter also cited California’s failure to meet its construction schedule, provide sufficient financial contributions and demonstrate that it was “effectively managing” the project.

Batory wrote that the high-speed rail authority reported spending only $48 million in December, far short of the $142 million officials committed to design and construction activities, and that “other months show the same shortfall of expenditures as compared to the state contribution commitment.”

He said the Federal Railroad Administration had determined that California would be unable to meet its 2022 deadline to complete the first section of track from Madera, north of Fresno, to Shafter, near Bakersfield. The agency is “exploring all available legal options,” Batory wrote, to recover more than $2 billion of stimulus money that it awarded in 2010 for the project.

Newsom made his comments about limiting high-speed rail during his State of the State address Feb. 12. He quickly backpedaled, insisting he still wanted to extend the Central Valley line to the Bay Area and Southern California. The governor said he just wanted to get the Central Valley segment, which is under construction, up and running first.

The rail project, which broke ground in 2015, remains tens of billions of dollars short of full funding.

In a statement Tuesday, Newsom said, “It’s no coincidence that the administration’s threat comes 24 hours after California led 16 states in challenging the president’s farcical ‘national emergency.’ The president even tied the two issues together in a tweet this morning.”

The reference was to a tweet in which Trump asserted that with cost overruns that “are becoming world record setting,” California’s project “is hundreds of times more expensive than the desperately needed Wall!”

The failed Fast Train project in California, where the cost overruns are becoming world record setting, is hundreds of times more expensive than the desperately needed Wall! — Donald J. Trump (@realDonaldTrump) February 19, 2019

California joined 15 other states to file suit against the Trump administration on Monday for declaring a national emergency to secure funding for his proposed wall along the U.S.-Mexico border without going through Congress.

“This is clear political retribution by President Trump, and we won’t sit idly by,” Newsom said. “This is California’s money, and we are going to fight for it.”

Federal and state Republican lawmakers, including McCarthy, applauded the Trump administration’s letter and called for Newsom to scrap the high-speed train entirely.

“The funds should be redirected to Central Valley infrastructure projects that will benefit the entire state,” Assemblyman Vince Fong, R-Bakersfield, said in a statement.

Kurtis Alexander and Alexei Koseff are San Francisco Chronicle staff writers. Email: kalexander@sfchronicle.com, alexei.koseff@sfchronicle.com Twitter: @kurtisalexander, @akoseff