President Trump has aggressively intervened in New York City affairs. He shocked Columbia University by stripping away government grants and contracts and demanding an overhaul of its admissions and disciplinary rules.

His administration threatened to cut off funding to the Metropolitan Transportation Authority unless it provided a long list of statistics on subway crime.

And even before he took office, Mr. Trump had his sights on congestion pricing.

Trump officials have given New York until Friday to end the embattled tolling program. It aims to reduce traffic and pollution while raising billions for public transit but has drawn opposition.

New York leaders have vowed to continue charging the tolls. And while the March 21 deadline is largely symbolic, it could be a prelude to a broader legal and political battle that could drag out for years.

On Tuesday, Sean Duffy, the U.S. transportation secretary, sent a letter to the M.T.A. raising concerns about crime on the subway and seeking data, most of it already publicly available. While he made no mention of congestion pricing, some transportation and legal experts questioned the timing of the letter and whether it was a thinly veiled attempt to get more leverage over the M.T.A.

“It’s entirely possible that this is a means to a predetermined end,” said Justin Balik, a former city transportation official who is now a vice president at Evergreen Action, an environmental advocacy group. “There is a gun to the head of mass transit and sustainable policy in general,” he added.