Caltrain passengers make their way to the station in San Francisco. The Transportation Department had agreed to spend more than $700 million on an electrification upgrade to the Northern California system. Transportation Secretary Elaine Chao signed off on the project Monday. (Nick Otto/for The Washington Post)

The Federal Transit Administration said Monday that it would sign off on a controversial California transit project, one of 21 for which Congress provided funding this month.

The proposal to electrify trains on the peninsula into San Francisco caused dissension among the state’s congressional delegation as House Railroad Subcommittee Chairman Jeff Denham objected to the plan while both of the state’s U.S. senators supported it.

“I think there is an issue that the California delegation needs to come together and discuss,” Transportation Secretary Elaine L. Chao said at a Senate hearing last week. “There appears to be split opinions on this project.”

Split opinions not withstanding, Congress approved funding for Caltrain’s $1.75 billion electrification project and 20 other transit projects in an omnibus bill signed by President Trump this month. All of the projects were described by Congress as either ready to start immediately or able to break ground later this year.

The Transportation Department said the rest of the projects approved by Congress were “advancing toward” approval as state and local authorities submitted final paperwork.

The Trump administration has suggested it has no plans to sign off on future transit investments, saying they should be funded by the local governments that benefit from them.

The three priciest projects on the list funded in the omnibus bill this month are the Purple Line light-rail project in Maryland, an extension of a light-rail system in Seattle, and the Caltrain plan to put electric trains on a corridor leading into San Francisco that now is served by diesel locomotives.

Supporters of building a 16-mile light-rail Purple Line in the Maryland suburbs say it should be first in line for a Trump administration that has called for shovel-ready infrastructure projects, particularly those that include private investment. The project, however, was dealt another setback Monday when a judge ordered federal transit officials to redo part of its environmental impact statement.

Also approved by Congress but awaiting final approval at DOT are transit projects in New York, Texas, Arizona, Florida, Indiana, Michigan, Missouri and New Mexico.

The projects have cleared multiple federal hurdles to reach this moment of final decision.

At the outset, a state or local government or transit agency applies for admission to the Capital Investment Grant (CIG) program. Once the project advances during the design phase, there is a second application seeking to be rated or scored by the U.S. Department of Transportation.

The DOT forwards those ratings to Congress with its recommendations for funding. (The Obama administration did this for the 16 projects last year.) Congress considers its current funding obligations for multiyear capital projects and selects those it thinks it can afford for a program that usually is budgeted at about $2.3 billion per year.

Congress completed that process with passage of the omnibus bill May 4, which funds both existing and new projects for the fiscal year that ends Sept. 30.

The final step, normally considered a formality, is the signing of a Full Funding Grant Agreement (FFGA), which stipulates the percentage the federal government will pay toward the total cost of a project and how much money it will provide each year. Most projects take several years to complete, and the agreement binds the federal government to keep its commitment until the project is finished.

The bottom line on the multiyear transit projects in question is about $8.5 billion, and the federal government normally pays about 40 percent of that amount.

At a hearing last Wednesday, Sen. Kamala D. Harris (D-Calif.) told Chao that the Caltrain project is “ready to start construction immediately.”

Harris responded to Monday’s announcement by saying that “Secretary Chao has done the right thing and committed the federal government to fulfill its obligation to see this project through completion.”

Rep. Anna G. Eshoo (D-Calif.), whose district includes part of the rail line, called the decision “a clear victory for my constituents and the people of the Bay Area.”

“It will enhance the spine of the Silicon Valley transportation system,” Eshoo said. “It’s a win for the environment.”

In March, the American Public Transportation Association wrote Chao about the Caltrain delay, noting that “no project has failed to secure final signature after successfully meeting evaluation criteria.”

On Friday, 25 Democratic senators and Bernie Sanders (I-Vt.) sent Chao and Mick Mulvaney, director of the Office of Management and Budget, a letter urging them to “immediately advance the billions in shovel-ready public transportation projects around the country that could break ground this year.”

The letter said, “Many Americans voted for the president based on his promise to rebuild our nation’s infrastructure. We urge you to keep that promise by funding and advancing the billions in transit projects currently in the CIG program’s pipeline.”

A senior Senate official, who said that Chao’s response at the hearing “made sense to nobody up here” on Capitol Hill, added, “This is proof positive that it’s pure incompetence in the Trump administration — not red tape — that’s holding up billions of dollars in job-creating projects.”

Both Maryland senators, Benjamin L. Cardin (D) and Chris Van Hollen (D), signed the letter to Chao and Mulvaney.

The Purple Line was five days from getting a full funding grant agreement for $900 million in August when a court order in a federal lawsuit made it ineligible for the federal grant.

Maryland officials have said construction on the line could begin within a few weeks after the environmental approval is restored and federal money begins to flow. Construction on the east-west line between Prince George’s and Montgomery counties was initially scheduled to start in October.

Maryland Transportation Secretary Pete K. Rahn said that as of June 1, the state will have to suspend much or all of the project’s pre-construction work unless it sees a “foreseeable path to resolving the litigation” and gets a “clear indication of when an FFGA may be executed,” according to a recent court filing in the lawsuit.

Rahn said the state is running out of state money being spent in anticipation of being reimbursed with the federal funding. If work is suspended, he said, the state would have about 60 days to get its environmental approval restored before it probably would have to cancel the project.

If the project is canceled, Rahn wrote, the state would lose more than $800 million, both in sunk costs and financial penalties to a team of private companies that has a $5.6 billion contract to build, operate, maintain and help finance the line in a 36-year public-private partnership.

About 200 engineers, designers and consultants are working on the line’s final design and engineering, state officials have said.

Congress already appropriated $325 million for the Purple Line over the past three fiscal years, but Maryland officials can’t access that money unless Chao signs the Full Funding Grant Agreement. Maryland officials have said the state can’t afford to build the Purple Line without federal funding.

The Trump administration could refuse to sign any new funding agreements and sit on any money that Congress has already appropriated to a project, transit advocates say.