US Transportation Secretary Sean Duffy said the move would halt a program that "leaves drivers without any free highway alternative, and instead, takes more money from working people to pay for a transit system and not highways".
Under the program, which launched on January 5, most passenger vehicles are charged $US9 ($A14) during peak periods to enter Manhattan south of 60th Street.
Trucks and buses pay up to $US21.60. The fee is reduced by 75 per cent at night.
The Metropolitan Transportation Authority and a New York bridge authority quickly filed suit in Manhattan seeking to block the move.
They said the decision was made "for blatantly political reasons" - to uphold a campaign promise of Republican US President Donald Trump.
Trump touted the move on social media and wrote: "LONG LIVE THE KING!" and the White House posted a mock photo of him on social media wearing a crown.
New York Governor Kathy Hochul has said that funds raised from the program would underpin $US15 billion in debt financing for mass transit capital improvements.
On Wednesday, she said the program had been a huge success, reducing commuting times and helping kids on school buses get to classes on time.
"We are a nation of laws, not ruled by a king," she said in a statement. "We'll see you in court."
Congestion pricing, which the city has estimated would bring in $US500 million in its first year, was approved in the final months of former President Joe Biden's administration.
As it involved tolls on federal highways, it required US approval.
Transit officials say the program has cut commuting times and that inbound trip times on all Hudson River and East River crossings are now 10 per cent to 30 per cent faster or more, while bus service has also improved.
Subway ridership also has grown since the toll was introduced.
Before the fee, New York said more than 700,000 vehicles entered central Manhattan daily, slowing traffic to 11km/h on average, which is 23 per cent slower than in 2010.
with AP
