In a major blow to a 15-year-long effort to modernize Caltrain, federal transit officials on Friday said they are withholding $647 million the agency was counting on this month to start work on a project to electrify the train line between San Francisco and San Jose.

The decision by the Federal Transit Administration comes just weeks after California’s Republicans in Congress asked the Trump administration to block the funds in an effort to halt one of California’s most controversial public works projects: high-speed rail.

In a letter Friday to the board that runs Caltrain, the FTA said it needed “additional time to complete review of this significant commitment of Federal resources,” and would make a final decision after President Donald Trump releases his budget for the 2018 fiscal year, which starts on Oct. 1.

Caltrain officials say the delay could have dire consequences for the $2 billion electrification project as they needed the funding by March 1. Replacing the line’s diesel trains with cleaner electric ones would allow the agency to run longer and more frequent trains and boost daily riders from 65,000 to 110,000.

“Deferral of the decision to execute the (grant) will prevent Caltrain from issuing the notice by this date and may jeopardize the viability of the project itself,” the statement said.

The delay comes on the heels of a request from California’s GOP delegation to block the funds pending an audit of the bullet train from San Francisco to Los Angeles, which would use the electrified train’s infrastructure. The California High-Speed Rail Authority has invested $700 million in Caltrain’s electrification project.

“Here’s the irony,” said Carl Guardino, CEO of the Silicon Valley Leadership Group that has long championed the electrification project. “This opposition was intended to stop high-speed rail. It’s only a flesh wound to high-speed rail, but it could be a mortal wound in our efforts to electrify Caltrain.”

Without the electrification project, congestion on Bay Area roads will continue to build and there could be far-reaching economic impacts, said Guardino, adding that the companies along the 45-mile Caltrain corridor generate 14 percent of the state’s GDP. It’s also where 43 percent of the country’s venture capital is invested.

Supporters of the project say it also will achieve one of President Trump’s major initiatives: create jobs. Caltrain has estimated the project would create 9,600 jobs in the Bay Area and throughout the country. For example, they say, a plant would be built in Salt Lake City to assemble the new rail cars.

Congressman Tom McClintock, R-Roseville, could not be reached Friday evening for comment on the FTA’s decision. But last week, when asked about the delegation’s request to block funding for the electrification project, he responded with an email about the high-speed rail project.

“This has never made any sense,” he said, referring to the high-speed rail project. “I have never supported a dollar of state funding going for this project and would never support a dollar of federal funding.”

The electrification and high-speed rail projects are intertwined but they are also distinct, as determined by a judge and the state Legislature, Guardino said. It’s a point he and other backers will look to drive home in the coming weeks.

“We will continue to try to replace dogma with data,” he said, “but we’re also going to engage the FTA, the secretary of transportation, the new presidential administration and our Republican congressional delegation as to why the electrification of Caltrain needs to be separated from a different project they don’t like.”

The grant proposal to transform Caltrain’s aging diesel fleet had been under review for two years, received a medium-high rating, and awaited a signature from the Secretary of Transportation, typically a pro-forma step.

The decision to defer funds drew a sharp rebuke from Congresswoman Anna Eshoo.

“I never imagined that the electrification of a train would be subjected to such brutal, partisan politics,” said Eshoo, D-Palo Alto, 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.”