NEW YORK — A federal judge on Wednesday blocked the Trump administration from withholding tens of millions of dollars in funds meant to protect subway riders from terrorism — noting the money became critical to New Yorkers’ safety after “3,000 people died within sight of this courthouse.”

In issuing his ruling, Manhattan Federal Judge Lewis Kaplan recalled the Southern District of New York courthouse serving as a staging area in the aftermath of the September 11 attacks on the World Trade Center in 2001.

“Obviously, New York State is no stranger to risks of terrorism attacks, and it’s not just 9/11 that tells us that,” the judge said at a hearing on a emergency motion filed by the state attorney general, listing several fatal acts of terrorism in the city before and after the attacks on the Twin Towers.

The ruling came after AG Tish James on Tuesday sued the Department of Homeland Security and the Federal Emergency Management Agency (FEMA) over the decision to withhold more than $33.8 million from the MTA because of New York’s laws protecting undocumented immigrants.

Kaplan granted the AG’s request for a temporary restraining order to stop the government from withholding the money and giving it to other states. His order will remain in effect until Oct. 15, by which time he’ll consider issuing a longer term injunction.

Kaplan said it appeared “likely, quite likely” that the AG would prove the Trump administration withheld the funds not because of the city’s risk level, but because it thinks “New York should be punished” for refusing to assist with what it calls “the largest deportation plan in history.”

The MTA cuts are separate from the Trump administration’s defunding of antiterrorism resources for the NYPD and the FDNY, moves the NYPD has blasted as “dangerous.” A separate lawsuit has been filed over those reductions.

“New Yorkers lived through the worst terrorist attack in our nation’s history, and we know what is at stake here,” James said in a statement.

Congress created the Transit Security Grant Program, which allocates the funds, in 2007 in response to the Sept. 11, 2001, terrorist attacks on the Twin Towers, aiming to protect New York’s tunnel network and subway stations from chemical, biological, radiological, and explosive threats, improve evacuation protocols, and finance other critical security measures.

The program has been operated by DHS and FEMA, who are required by statute to do so, as Tuesday’s suit details.

DHS said it was slashing the funding over New York City and State’s status as sanctuary jurisdictions and the refusal to devote scarce law enforcement resources to augment civil immigration enforcement by the federal government.

It was made despite the MTA’s network carrying more than 5 million riders daily— amounting to nearly 40% of commuters across the entire U.S. — and facing some of the highest threats nationwide.

It also came despite President Trump’s comments this year expressing concern over subway safety, an evergreen issue for New Yorkers.

“Women can’t ride the subway without worrying that a hoodlum will shove them onto the train tracks,” he said in remarks to the Department of Justice in March. “I used to take the subway. I used to feel safe. When I was young, I’d go to the — my parents would drop me off at the subway. I’d take the subway to my school. Can you believe it? Today, they wouldn’t be doing that.”

As of Wednesday, his administration is cutting 100% of federal funds dedicated to protecting riders from terrorism.

The president foreshadowed the cuts on his first day in office when he directed DHS to “ensure that so-called ‘sanctuary’ jurisdictions do not receive access to Federal funds,” which he said were in “lawless insurrection.”

The AG’s suit said the office didn’t learn about the decision until reading about it in Streetsblog on Tuesday morning.

The Trump administration’s cuts to terrorism-fighting funds for New York could have impacts beyond the underground.

DHS Secretary Kristi Noem has defunded antiterrorism programs in New York by a total of around $187 million, defunding the NYPD, the FDNY and the Joint Task Force Empire Shield by slashing resources allotted through the Homeland Security Grant Program.

Twelve Democrat-led states including New York filed suit in Rhode Island Monday seeking to stop those cuts.

Gov. Hochul, who wrote to Noem Tuesday, called the move “incredibly dangerous” and said it would leave New York exposed “at a moment when our threat environment needs us more than ever.”

“I call upon you to be transparent with what appears to be a politically motivated effort to reduce funding for New York,” Hochul wrote. “This decision serves only to make not just New York but all of America more vulnerable to terrorist attacks.”

James sought information about the cuts but in place of an explanation, the AG’s office received a PowerPoint presentation by Congressional staff that said the MTA would be the only applicant denied funds, which would beef up awards to other applicants, according to the suit. The reason given was New York’s sanctuary status.

The decision is illegal as it is outside DHS’s authority and violates the Constitution and the Administrative Procedure Act, standing contrary to the statute under which the program was created, which designates eligibility solely based on the risks of terrorist attacks, the AG’s suit argues.

“This is only the latest in a string of attacks,” Tuesday’s suit reads. “Since January 2025, Defendants have engaged in a concerted campaign to pressure States, including New York, to serve as enforcers of federal immigration law, subverting the design of DHS grant programs.”

A spokeswoman for DHS did not immediately respond to a request for comment.

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