The head of the federal Department of Transportation promised on Thursday to take away control of the project from the Metropolitan Transportation Authority.

“President Trump has made it clear: the days of reckless spending and blank checks are over,” Mr. Duffy said in a news release. 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.