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In the end, Secretary Chao heeded the Republican letter's arguments, and deferred the grant in a letter written by FTA Executive Director Matthew Welbes to Caltrain which stated the FTA needed "additional time to complete review of this significant commitment of Federal resources".<ref name=SMDJ-170218>{{cite news |url=http://www.smdailyjournal.com/news/local/electrification-funds-in-peril-federal-transit-administration-delays-million-caltrain/article_16d7f9d6-7ea3-52b7-992d-cf3528c708fe.html |title=Electrification funds in peril: Federal Transit Administration delays $647 million Caltrain decision |author=Weigel, Samantha |date=February 18, 2017 |newspaper=[[San Mateo Daily Journal]] |access-date=April 4, 2017}}</ref><ref name=SFC-170217>{{cite news |url=http://www.sfgate.com/bayarea/matier-ross/article/Trump-administration-deals-a-big-setback-to-10941880.php |title=Trump administration deals a big setback to Caltrain |author1=Matier, Phil |author2=Ross, Andrew |date=February 17, 2017 |newspaper=[[San Francisco Chronicle]] |access-date=March 25, 2017}}</ref> Caltrain had expected Secretary Chao to approve the grant and sign the grant agreement by March 1, which is normally a ''[[pro forma]]'' step performed after the thirty-day comment period for a highly rated project, and had already awarded construction contracts.<ref name="contractextension"/><ref name="SV">{{cite news|url=http://www.eastbaytimes.com/2017/03/24/trump-chao-get-an-earful-on-caltrain-funds/|title=Trump, Chao get an earful on Caltrain funds from Silicon Valley leaders|newspaper=[[East Bay Times]]|author=Richards, Gary|date=March 24, 2017|access-date=March 29, 2017}}</ref> [[Balfour Beatty Construction]] and [[Stadler Rail]] had already begun preparations to upgrade the existing tracks and build electrical trainsets, respectively. Caltrain negotiated an emergency four-month contract extension at a potential cost of $20 million.<ref name="contractextension"/><ref name=SFC-170227>{{cite news |url=http://www.sfgate.com/bayarea/article/Caltrain-acts-to-keep-electrification-plan-alive-10964012.php |title=Caltrain acts to keep electrification plan alive |author=Cabanatuan, Michael |date=February 27, 2017 |newspaper=[[San Francisco Chronicle]] |access-date=March 25, 2017}}</ref> Under the preliminary budget proposal released in mid-March 2017, the [[United States Department of Transportation]]'s Capital Investment Grant Program would be eliminated, although approved projects would continue to be funded.<ref name=SFC-170317 /> Since Secretary Chao had withheld grant approval for the electrification project, its future fell into doubt.<ref name=SFC-170317 />
In response to the grant deferral, various local officials traveled to [[Washington, D.C.]], to lobby federal officials to release the money. Editorials in local and national newspapers urged approval of the grant, including the ''[[Sacramento Bee]]'', which called the deferral "a petty attack",<ref>{{cite news |url=http://www.sacbee.com/opinion/editorials/article140446843.html |title=House Republicans launch a petty attack on a smart rail project |author=Editorial Board |date=March 24, 2017 |newspaper=[[Sacramento Bee]] |access-date=March 28, 2017}}</ref> the ''[[East Bay Times]]'', a noted CHSRA detractor,<ref>{{cite news |url=http://www.eastbaytimes.com/2017/02/24/editorial-feds-should-electrify-caltrain-kill-bullet-train/ |title=Editorial: Feds should electrify Caltrain, kill bullet train |author=Editorial Board |date=February 24, 2017 |newspaper=[[East Bay Times]] |access-date=March 28, 2017}}</ref> and ''[[The New York Times]]'', which called the delay "counter to Mr. Trump's campaign promises of increased infrastructure spending."<ref>{{cite news |url=https://www.nytimes.com/2017/03/13/opinion/a-silicon-valley-train-gets-stuck.html |url-access=subscription |title=A Silicon Valley Train Gets Stuck |author=Editorial Board |date=March 13, 2017 |newspaper=[[The New York Times]] |access-date=April 5, 2017}}</ref> Henry Grabar noted the grant deferral could be "an early test of a simmering fear that the state's outspoken political opposition to the Trump administration might come with a price".<ref name=Slate-Grabar>{{cite web |url=http://www.slate.com/blogs/moneybox/2017/02/16/will_elaine_chao_axe_federal_funding_for_caltrain.html |title=If Elaine Chao Axes This Bay Area Rail Funding, We'll Know She's Politicizing Transportation |author=Grabar, Henry |date=February 16, 2017 |work=[[Slate (magazine)|Slate]]: Moneybox (blog) |access-date=March 28, 2017}}</ref> San Jose Mayor [[Sam Liccardo]] met with Department of Transportation officials, urging them to upgrade a system that "was built under the presidency of [[Abraham Lincoln]]". Additionally, more than 120 Silicon Valley business leaders sent a letter to Secretary Chao, asking her to explain "the last-minute attempt to derail two decades of work".<ref name="SV"/> In early March, California Governor [[Jerry Brown]] sent a letter to Secretary Chao, asking to discuss the funding grant,<ref name=EBT-170303>{{cite news |url=http://www.eastbaytimes.com/2017/03/03/call-me-jerry-brown-urges-trump-administration-to-fund-caltrain-project/ |url-access=subscription |title=Call me? Jerry Brown urges Trump administration to fund Caltrain project |author=Murphy, Katy |date=March 3, 2017 |newspaper=[[East Bay Times]] |access-date=March 28, 2017}}</ref> and subsequently met with Secretary Chao and Representative McCarthy, urging them to reconsider the funding deferral, saying afterward that he was "cautiously optimistic" that the money would be released.<ref>{{cite news|url=http://www.sacbee.com/news/politics-government/capitol-alert/article139943463.html |first1=Christopher |last1=Cadelago |title=Jerry Brown meets with Republicans, 'cautiously optimistic' about Caltrain approval|newspaper=[[Sacramento Bee]]|date=March 21, 2017|access-date=March 29, 2017}}</ref>
On April 30, legislators in the U.S. Congress released the proposed 2017 federal budget, which included partial funding for the electrification project, but restricts its distribution unless Secretary Chao signs off on the grant.<ref>{{cite web|url=https://rules.house.gov/sites/republicans.rules.house.gov/files/115/OMNI/DIVISION%20K%20-%20THUD%20SOM%20OCR%20FY17.pdf|title=Transportation, Housing and Urban Development, and Related Agencies Appropriations Act, 2017 |publisher=U.S. House of Representatives|access-date=May 2, 2017|archive-url=https://web.archive.org/web/20170502011347/https://rules.house.gov/sites/republicans.rules.house.gov/files/115/OMNI/DIVISION%20K%20-%20THUD%20SOM%20OCR%20FY17.pdf|archive-date=May 2, 2017|url-status=dead}}</ref> The proposed budget includes $100 million of the $647 million grant, with the balance expected in future years. Secretary Chao claimed she could not sign the grant without the full grant being budgeted, which was disputed by Caltrain and both California Senators [[Dianne Feinstein]] and [[Kamala Harris]].<ref>{{cite news |url=http://www.mercurynews.com/2017/05/17/elaine-chao-caltrain-grant-hearing/ |title=Transportation Secretary Elaine Chao says she can't approve Caltrain electrification grant yet |author=Tolan, Casey |date=May 17, 2017 |newspaper=San Jose Mercury News |access-date=May 19, 2017}}</ref> On May 22, the FTA announced its intent to sign the funding grant, restoring the final piece of funding for the electrification project.<ref>{{cite news |url=http://www.sfexaminer.com/feds-flip-will-approve-funding-caltrain-electrification/ |title=Feds flip, will approve funding for Caltrain electrification |author=Rodriguez, Joe Fitzgerald |date=May 22, 2017 |newspaper=San Francisco Examiner |access-date=May 22, 2017 |archive-date=May 23, 2017 |archive-url=https://web.archive.org/web/20170523152650/http://www.sfexaminer.com/feds-flip-will-approve-funding-caltrain-electrification/ |url-status=dead }}</ref> The official grant was finally signed on May 23.<ref>{{cite news|title=It's officially done. Caltrain's GM, Jim Hartnett, signed the FFGA @USDOT this morning.|url=https://twitter.com/Caltrain/status/867083183820611584|access-date=May 28, 2017|work=Official Caltrain [[Twitter]] Account|date=May 23, 2017}}</ref>
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