A federal judge is temporarily blocking the Trump administration from withholding funding from New York in a battle over a congestion pricing scheme that levies additional taxes on drivers driving into certain parts of Manhattan.

Judge Lewis Lian issued a restraining order against the federal government on Tuesday afternoon. He said the Metropolitan Transportation Authority would probably suffer “irreparable harm” with the elimination of the tolls. The state agency runs mass transit in the city and oversees the new tolls.

The ruling means the program will likely continue as the legal battle plays out.

The $9 toll to enter Midtown and Lower Manhattan went into effect on January 5 after Governor Hochul delayed its implementation until after the 2024 election. The program is designed to reduce gridlock and raise money to fund improvements to the city’s crumbling mass transit system.

President Trump has been an ardent opponent of the first-in-the-nation tax and has vowed to kill it. His transportation secretary, Sean Duffy, rescinded federal approval for the program in February, calling it “a slap in the face to working class Americans and small business owners,” and initially gave New York until March 21 to comply.

The MTA sued, and Mr. Duffy pushed the deadline back to April 20. Ms. Hochul refused to end the tolls and they remained in place past the deadline. The new restraining order will allow the tolls to continue until at least June 9 and bars Mr. Duffy for retaliating against the state.

About 560,000 vehicles per day entered the congestion zone in March, a 13 percent drop from the roughly 640,000 the MTA projects would have driven through the area without the tolls, according to data the agency released last month.

The agency has previously said it’s on track to meet the $500 million in revenue initially projected this year from the congestion tax.