In the first big hit to the Bay Area from the Trump administration, newly minted Transportation Secretary Elaine Chao has put the brakes on $647 million for Caltrain to go electric — and in the process pretty much killed hopes for high-speed rail coming to San Francisco anytime soon.

“It puts the (electrification) project in serious jeopardy,” Caltrain spokesman Seamus Murphy said Friday.

Caltrain carries about 60,000 riders a day between the South Bay and San Francisco, but its diesel-driven trains are both costly to operate and slow. Officials see electrification as a way both to increase ridership and save money on operating costs.

Going electric would also allow the Peninsula line to be the final link in the high-speed rail system that Gov. Jerry Brown wants to stretch from San Francisco to Los Angeles. The Obama administration embraced the idea, but California Republicans have long portrayed it as a boondoggle and sought to kill it.

In a Jan. 24 letter to Chao, all 14 Republicans in the state’s congressional delegation called for the Caltrain money to be put on hold until a full audit is done on high-speed rail. On Friday, Chao obliged — the Federal Transit Administration, which she oversees, said a decision on the $647 million federal grant needed to keep the project going would be delayed.

Matthew Welbes, the agency’s director, told Caltrain officials in a letter that the delay would allow the grant “to be considered in conjunction” with President Trump’s upcoming budget proposal for fiscal 2017-18.

The delay doesn’t kill the project by itself. But officials of the Peninsula Corridor Joint Powers Board, which runs Caltrain, say it all but derails electrification.

That’s because Caltrain has already selected contractors for the electrification project. “We have a March 1 deadline to start issuing contracts,” Murphy said.

After that, Caltrain will have to start the bidding process all over again — which could result in a much costlier set of contracts.

And of course, there’s the huge question of whether Trump will even put the Caltrain money in his budget.

“I never imagined that the electrification of a train would be subjected to such brutal, partisan politics,” Rep. Anna Eshoo, D-Palo Alto, whose district includes several Caltrain stations, said in a statement. “This is not a Democratic project nor is it a Republican project. It is about the modernization of an outdated commuter system that is the spine of the transportation system of the Peninsula and the Silicon Valley region.”

Eshoo added that Caltrain electrification “is a shovel-ready project which would create thousands of jobs in the Bay Area and employ thousands in other states. It would be built by American workers and built with American products.”

In his letter, Welbes said federal officials were aware of Caltrain’s March 1 deadline, but that Washington needed “additional time to complete review of this significant commitment of federal resources.”

Caltrain has already spent $150 million on planning to go electric, but without the federal and matching funds, the overall $1.98 billion project will go into limbo.

As for high-speed rail, a $64 billion (and counting) endeavor that is still not fully funded, its viability would take a big hit if bullet trains went no farther north than the South Bay.

The state High Speed Rail Authority’s chairman, Dan Richard, had little to say about the federal action Friday beyond, “We are evaluating our options.”

San Francisco Chronicle columnists Phillip Matier and Andrew Ross normally appear Sundays, Mondays and Wednesdays. Matier can be seen on the KPIX TV morning and evening news. He can also be heard on KCBS radio Monday through Friday at 7:50 a.m. and 5:50 p.m. Got a tip? Call (415) 777-8815, or email matierandross@sfchronicle.com. Twitter: @matierandross