Passengers at the L'Enfant Plaza Metro station in Washington. (Linda Davidson/The Washington Post)

The federal government on Friday began to withhold millions of dollars in transportation funding from Virginia, Maryland and the District because they missed a deadline to create an independent safety agency to oversee Metro.

In a letter to governors Terry McAuliffe (D-Va.) and Larry Hogan (R-Md.) and D.C. Mayor Muriel E. Bowser (D), the Federal Transit Administration said it was withholding money that would affect a range of transit projects, from bus service in Richmond to Baltimore’s subway.

But the biggest chunk — more than $4 million, according to state officials — was money that would have flowed to the struggling Metro system between now and September.

The FTA said it will not allocate any of the federal funds, which it estimates would total as much as $15 million over a full fiscal year, until the oversight commission is established.

Elected officials said the decision by Transportation Secretary Elaine Chao underscored the need to move quickly on Metro reforms.

“I don’t agree with docking transit funds for regions of Virginia far from D.C. with their own transportation needs — including Hampton Roads, Richmond, and Roanoke — but this is another reminder of why it’s crucial to act on [Metro] safety,” said Sen. Tim Kaine (D-Va.).

Rep. Gerald E. Connolly (D-Va.) said he was surprised to see the agency move so quickly to penalize the three jurisdictions but said he is also sympathetic with FTA’s frustrations at the region’s slow progress to strengthen safety oversight of Metro.

“I applaud the FTA for keeping the focus on safety and how critical it is that we proceed with all due speed,” Connolly said, “but they could have been more mindful of the challenges we faced in the legislative process.”

Maryland’s two U.S. senators, Democrats Benjamin L. Cardin and Chris Van Hollen, said in a joint statement that withholding transit funds was counterproductive. “Cutting off resources for projects midstream will affect safety and increase overall costs, which is exactly the opposite of what FTA should be trying to accomplish,” they said. “We understand that a deadline has been missed, but we urge the FTA to rethink this course of action in the name of safety and stability of our regional transportation system.”

In the letter, Matthew Welbes, FTA’s executive director, outlined the steps needed for the new safety agency to be certified. He also reminded the jurisdictions of their obligations.

“By law, states have the primary responsibility for overseeing the safe operation of their rail transit systems, not only for riders but for transit operators and workers,” he wrote. “FTA has been providing oversight for . . . Metrorail since October 2015, but the role is temporary. We will continue to direct safety oversight of Metrorail only until the District of Columbia, Maryland and Virginia step up and establish an FTA-certified State Safety Oversight Program.”

Of the three, only the District has passed the legislation need to create the new safety body, which Bowser signed into law Friday. The mayor is expected to meet with Chao on Monday.

“We did our part first and encourage our partners to follow our lead,” Bowser spokesman Kevin Harris said.

Del. Eleanor Holmes Norton, (D-D.C.) blasted the move.

“The FTA’s decision to punish the District of Columbia, Maryland and Virginia by withholding transit funds from [Metro] and other regions of the states with their own transit needs is unfair and counterproductive,” she said.

The jurisdictions had been given until Thursday to create the new agency, but officials in Maryland and Virginia said because of their legislative calendars they were unlikely to meet the deadline set by then-Transportation Secretary Anthony Foxx.

Foxx, frustrated with the slow pace, imposed the deadline a year ago in hopes of prodding officials into action. The new safety agency would replace a previous oversight body, the Tri-State Oversight Committee, which was widely viewed as a failure.

But with the change of administrations, it was up to Chao to decide whether to act on Foxx’s threat of withholding 5 percent of federal funds that are supposed to flow annually to the states and city as part of a federal formula.

“The Governor is disappointed in this action, which will impact Metro and transportation projects across the Commonwealth,” Brian Coy, a spokesman for McAuliffe, said in an email.

Even a temporary loss of funds could have a significant impact on projects, officials said.

“Federal formula dollars support Metro’s capital program, which is critical to the safety and maintenance of train and bus service,” said Metro spokesman Dan Stessel via email. “We will work closely with the funding jurisdictions to determine how best to make up the difference to avoid reducing safety or reliability projects.”

The Metro board chairman, Jack Evans, warned that withholding even just 5 percent of federal funds could have a significant financial effect on Metro, which is already looking at raising fares and cutting service to close a $290 million gap in its operating budget.

“Starving Metro of money is not only a bad idea — it’s a stupid idea. Metro needs all the money we can get, particularly on the capital side,” Evans said. “That’s money we now cannot use to repair the system. So how does that make Metro a better system?”

In Virginia, officials expected $6.2 million to be withheld, more than half of which would come from projects in Northern Virginia. The bulk of that money, $3.4 million, is allocated directly to Metro by the Northern Virginia Transportation Commission. The Virginia Railway Express, the area’s commuter rail service, could miss payments of up to $380,672.

In the District, the penalty would affect $795,000 in funding earmarked for Metro.

Maryland transportation officials said the state would temporarily forgo $4.8 million in fiscal year 2017 and the impact would be felt statewide. The Baltimore region, including the city of Baltimore, would temporarily lose nearly $3.3 million; Montgomery and Prince George’s counties, $725,984.

But Maryland officials indicated that if the new safety agency is in place by Sept. 30, there would be no impact on the state’s budget and they believed the federal government would restore the money retroactively.

Rep. Barbara Comstock (R-Va.) said she spoke with Chao on Thursday and received assurances that the secretary is committed to working on reforms that will make Metro safer and more reliable.

“The February 9th deadline was set up by the prior Administration without taking into account the legislative sessions of each jurisdiction,” Comstock added. “Those jurisdictions will likely pass the Metro Safety Commission legislation in short order. As long as the Metro Safety Commission becomes operational, the region will not lose any federal money.”

But some think it will take more than just a few months to meet all the requirements necessary for the FTA to sign off on the new agency. For that reason, the District’s Evans urged the FTA to release the money as safety oversight legislation is passed by Maryland and Virginia.

In Richmond, the full House approved the bill Tuesday by unanimous vote of 97 to 0 and the legislation now moves to the Senate. In Maryland, a House committee held a hearing on the bill Thursday, and it was expected to move to the full House within the next two weeks.

Aaron C. Davis, Peter Jamison, Robert McCartney, Josh Hicks and Laura Vozzella contributed to this report.