The head of the federal Department of Transportation said on Thursday that the Trump administration would take control of the $7 billion renovation of Pennsylvania Station away from the Metropolitan Transportation Authority.

The move appeared to be the latest salvo in a running confrontation between the Trump administration and New York’s transportation agency, which began when the federal transportation secretary, Sean Duffy, ordered the state to end its congestion pricing program.

The station, one of the busiest and also most maligned transit hubs in the world, has for decades been on the verge of a huge overhaul to remedy its cramped and dreary corridors. But the competing priorities of local, state and federal stakeholders have made progress difficult.

It was not immediately clear what the administration’s vision for Penn Station might look like, but federal officials stated a preference for Amtrak, the station’s owner, to partner with private investors on the renovation. Nor was it known whether the Trump administration supports one of the various proposals for renovating or expanding the station.

But Mr. Duffy did not miss an opportunity to disparage the M.T.A., charging that its leadership has mismanaged the project.

“President Trump has made it clear: the days of reckless spending and blank checks are over,” Mr. Duffy said in a news release. “New York City deserves a Penn Station that reflects America’s greatness and is safe and clean. The MTA’s history of inefficiency, waste and mismanagement also meant that a new approach is needed.”

In a statement, Gov. Kathy Hochul described the Trump administration’s decision as a boon for the state and indicated that she would withdraw more than $1 billion of funding from the project.

“In multiple meetings with President Trump, I requested that the federal government fund the long-overdue overhaul of Penn Station. Clearly that effort has been successful, and I want to thank the president and Secretary Duffy for taking on the sole responsibility to deliver the beautiful new $7 billion station that New Yorkers deserve.”

She added that the decision was “a major victory for New Yorkers, and the use of federal funds will save New York taxpayers $1.3 billion that would have otherwise been necessary for this project.”

Janno Lieber, the head of the M.T.A., said in a statement that the authority was glad the federal government is focusing on the transit hub, noting that the agency recently completed major work on the 33rd Street concourse of the station. He added that the M.T.A. expects to participate in the administration’s efforts. The authority did not receive an advance copy of Mr. Duffy’s announcement.

One of the biggest hurdles to renovating the train hall has been the structure that sits atop the station: Madison Square Garden, the famous sports arena whose owners have bristled at the thought of moving or disturbing the venue.

For years, the M.T.A., which is responsible for about two-thirds of the station’s 600,000 daily riders, has been in charge of the renovation plans. In 2023, the authority completed the new 33rd Street concourse for Long Island Rail Road and subway riders, a project that would serve as a model for the rest of the expansion. But conflicting priorities, including plans to expand train capacity by demolishing a mixed-use block near the station, have slowed progress.

Mr. Trump has the ultimate say over the station because it is owned by Amtrak, a corporation controlled by the federal government. Members of its board of directors are presidential appointees. All of the current directors were appointed by President Joseph R. Biden Jr., except the chairman, Anthony R. Coscia, who was appointed by President Barack Obama.

A few weeks ago, the White House pressured Amtrak’s chief executive, Stephen Gardner, to resign because of his ties to the Biden administration. Mr. Gardner has not been replaced.

Amtrak officials did not immediately respond to requests for comment.

Kris Kolluri, the chief executive of New Jersey Transit, whose trains run to and from Penn Station, said: “As one of the largest users of the station, N.J. Transit looks forward to working with U.S. D.O.T. and Amtrak on the Penn Station Reconstruction project.”

Despite the political undertones of the announcement, some transit supporters were cautiously optimistic about the Trump administration’s move.

“He could name it after himself if that’s what it takes,” said Tom Wright, the president and chief executive of the Regional Plan Association, a civic think tank that has long supported a renovation of the train hub. The federal government’s intervention could centralize the planning process and also mean that more private developers will compete in the process, he said.

In June 2023, Governor Hochul announced her commitment to choosing a plan for the station’s overhaul, but almost two years later, the state has yet to put out a formal request for proposals, despite the release of two plans that could be led by private developers.

A proposal from Halmar International, a developer, to demolish a portion of Madison Square Garden and make way for major transit improvements gained support from several elected officials in 2023. A competing vision, led by Alex Washburn, a former chief urban designer for New York City, would completely remove Madison Square Garden from the site, move it across the street and build both a new train hall and a sprawling park.

Other longtime observers were less enthusiastic.

“I am beyond skeptical that this federal government can manage a project of this size by seizing control while simultaneously slashing funding,” said Tony Simone, an assemblyman whose district includes the station. Mr. Simone recently proposed a development plan for the area that included additional housing and a park.

The announcement did not detail what the Trump administration’s vision for the site might look like, but a draft of an unsigned executive order on Penn Station gave some hints. The design would emphasize “classical architectural heritage” that would “ennoble the United States,” according to the order that The New York Times reviewed.

A transformation of Penn Station was a component of the sprawling Gateway project, which would add capacity for intercity and commuter trains to cross the Hudson River. The Gateway tunnels, which are being constructed, would complement the existing pair of single-track tunnels that are more than 110 years old and suffered from being flooded with brackish water when Hurricane Sandy struck in 2012.

The new tunnels would essentially double the number of trains that could cross the river during rush hours. There is not enough room at Penn Station for any more trains now, so Amtrak has proposed expanding the station to take up most of the block on the other side of West 31st Street to accommodate them.

But that block is occupied by apartments and businesses and a large Roman Catholic church, St. John the Baptist, which is more than 150 years old. Community activists and elected officials have opposed the plan to bulldoze the buildings there for years.

Other groups have urged transportation officials to solve the capacity problem by having more trains run through the station and turn around somewhere outside Manhattan. Some Amtrak trains do that now, but Long Island Rail Road and New Jersey Transit trains account for the vast majority of the train traffic at Penn.

Danny Pearlstein, a spokesman for the Riders Alliance, a transit advocacy group, said the timing of the letter suggests the federal government is interested in one-upping the M.T.A. just days before a deadline that Mr. Duffy gave the state to end its congestion pricing toll, a program the president has vowed to kill.

“They’re clapping back at the M.T.A. and New York in an irrational way,” Mr. Pearlstein said, adding that, had the administration cared about the project before the tolling feud, it would have pushed for investments in mass transit, its riders and its infrastructure.

“They’ve yet to show that they care about any of those things,” he said.