WASHINGTON — U.S. Transportation Secretary Elaine Chao isn’t budging on approving federal funds to help the Bay Area begin the electrification of Caltrain tracks.

Chao said at a hearing Wednesday morning of the Senate Environment and Public Works committee that she won’t sign off on a funding agreement necessary to release federal funds for the project, even as a critical June 30 funding deadline looms.

Caltrain is waiting for a $647 million federal grant for the electrification project, which would lead to faster and more reliable trains up and down the Peninsula. Before Trump took office, the grant had been through a multi-year approval process and was close to being finalized. But it’s been held up by the U.S. Department of Transportation after all 14 members of the Republican members of the California congressional delegation argued in a letter to Chao that it would go to bolstering the state’s high-speed rail project — which Republican politicians generally despise.

While bullet trains would run on the electrified track, supporters of the project say it’s necessary in its own right to keep Caltrain running with reasonable speed and reliability.

Responding to questions about the status of the grant from Sen. Kamala Harris, a California Democrat, Chao suggested that the Golden State is already getting more than its fair share of federal transportation dollars.

“Fifty percent of the New Starts in the budget, if I’m not mistaken, goes to California,” Chao said, referring to the New Starts transportation grant program. “California — and in particular Caltrain — is not the only project that’s waiting for this money.”

Chao said that she couldn’t sign the funding agreement with Caltrain until all the funds for the grant were appropriated by Congress.

The 2017 budget passed recently includes $100 million for the grant — but the full $647 million hasn’t been budgeted. “I cannot (sign the funding agreement) if the funding is not there,” Chao said.

But Caltrain said that that argument doesn’t hold water. Every grant “in the history of the program” has committed funding not yet appropriated by Congress, said Seamus Murphy, a spokesman for Caltrain. Usually, he said, the agreements specify funds that are expected to be appropriated in future years.

Chao said that the $100 million budgeted for Caltrain “will go out” to the state — and added that more than $118 million had been budgeted for the 2018 fiscal year.

But Murphy said that’s essentially meaningless if the Department of Transportation doesn’t approve the grant. Without Chao signing off, Caltrain can’t use any of the federal money.

“How do you suggest we resolve the problem?” Harris asked Chao during the hearing.

“I wish I knew,” Chao responded. “It is an issue I think the California delegation needs to come together and discuss, because there seems to be split opinions on this project.”

Murphy said it would put 10,000 people to work around the country, not just in California. “It’s the most shovel-ready transit project in the country,” he said.

The construction contracts for the program expire at the end of June. If the grant agreement isn’t signed by then, it’s back to the drawing board for Caltrain.

“At a minimum, we’d have to start over putting together a funding plan and awarding new contracts,” Murphy said. “It would definitely be a debilitating setback.”

Harris and California’s senior U.S. senator, Dianne Feinstein, issued a statement essentially agreeing with Murphy’s analysis and urging Chao to sign the agreement as soon as possible.

“All of the funding Congress makes available depends on signing this agreement,” the statement said.