In response to the Trump administration’s portrayal of the subway system as lawless, New York transit officials on Wednesday shot back: Crime is down, fare evasion is falling — and the nation’s largest transit system deserves far more money.

Janno Lieber, head of the Metropolitan Transportation Authority, said the agency would be taking “a very professional, fact-based approach” to the federal government’s demands last week for a list of statistics on transit crime, aiming to show that crime underground is the lowest it has been in more than a decade.

Still, a surge in unpredictable attacks in the subway remains troubling, M.T.A. officials acknowledged, and concerns about crime remain an obstacle to getting some riders to return. A January rider survey showed that a little more than half of subway customers — 56 percent — say they feel safe on trains.

New York transit officials have remained defiant weeks into their standoff with federal officials, which began when Washington demanded the halt of congestion pricing last month. When New York refused, the skirmish escalated, with Sean Duffy, the secretary of the U.S. Department of Transportation, threatening to defund transit projects, if the state did not provide the crime stats. Over the weekend, he referred to the subway system as a “shithole,” WNBC-TV reported, while repeating his demands.

A formal response to the secretary is in the works, but the transit authority wanted to preview the information, Mr. Lieber said at a board meeting on Wednesday.

“We’re going to stay coolheaded because the facts are on our side,” Mr. Lieber said.

Excluding 2020 and 2021, during the height of the pandemic when subway ridership was way down, last year had the fewest number of felonies reported in the transit system in 15 years, Michael Kemper, chief security officer at the M.T.A. and a former chief of transit at the Police Department, said at the board meeting. Weekly ridership has rebounded to about 75 percent of prepandemic levels.

During its rebuttal, the transit agency attempted to turn the tables and requested a larger share of federal transportation funding, at a time when it is trying to pay for its next five-year, $68 billion capital plan budget.

The transit agency receives between $1.5 billion to $2.5 billion a year from the federal government, which is used for improvements, like repairing outdated electrical equipment, as well as some basic maintenance, Mr. Lieber said.

John McCarthy, the chief of policy and external relations at the M.T.A., said the agency receives just 17 percent of a federal pool of transit funding, despite carrying 43 percent of the nation’s transit ridership.

“It’s shortchanging low- and middle-income New Yorkers,” he said.

In a statement, a spokeswoman for Mr. Duffy said a spate of recent violent crimes, including the death of a woman who was set on fire on the subway last year, has left riders on edge. “The M.T.A. can try and gaslight the American people, but attacks like these make every passenger fear becoming the next victim. It should have never gotten to this point for the governor and the M.T.A. to crack down on crime.”

Mr. Duffy demanded data on the number of assaults committed on passengers and employees; efforts to prevent “subway surfing,” the practice of riding moving trains; and the money spent on a number of security-related projects.

The back-and-forth over subway crime comes as the Trump administration and the M.T. A. are battling over congestion pricing in federal court. The tolling program, which began in January, charges most drivers $9 to enter the busiest section of Manhattan during peak hours. It has reduced traffic while aiming to raise $15 billion for critical transit repairs and upgrades.

Mr. Trump has vowed to kill congestion pricing, expressing concerns that the tolls would drive visitors and businesses away from Manhattan, though there is little evidence of that so far.

While Mr. Duffy did not mention congestion pricing while demanding the subway crime stats from the M.TA., a number of transit supporters questioned the timing of the request, which came shortly after Gov. Kathy Hochul reiterated her support for the tolling program.

Last month, Mr. Duffy withdrew federal authorization for congestion pricing, which was approved by the Biden administration. Federal officials initially gave New York until March 21 to stop charging the tolls, but last week Mr. Duffy offered a 30-day reprieve in a combative social media post, in which he described the program as a “slap in the face to hard working Americans.”

Mr. Duffy also put Ms. Hochul on notice that “your refusal to end cordon pricing and your open disrespect towards the federal government is unacceptable,” according to his post.

The M.T.A. has sued federal transportation officials and promised to keep collecting tolls unless a court orders it to stop. Legal and transportation experts have said that federal officials do not have the authority to reverse course now.

In raising the specter of crime in the subway system, Mr. Duffy is poking a sensitive topic among New Yorkers. The M.T.A. has said that, even as subway crime overall was declining, there was a rise in assaults underground.

In 2023, for the first time in nearly two decades, felony assaults outnumbered robberies in the subway, raising concerns that the nature of violence underground was becoming more unpredictable.

In recent months, a few high-profile crimes have shaken riders, including the one that Mr. Duffy’s spokeswoman referred to, when Debrina Kawam, a 57-year-old woman, died after being set on fire, as she slept on a train in December. Later that month, Joseph Lynskey was shoved in front of an oncoming train at the 18th Street station in Manhattan and survived. There were 10 murders in the subway in 2024, up from three in 2019.

Late last year, following an overnight slashing attack on an A train that injured a conductor, Ms. Hochul ordered 1,000 members of the National Guard to begin patrolling the subways. As of earlier this month, about 1,250 Guard members, M.T.A. officers and state police officers patrolled the system, according to the governor’s office. In addition, thousands of city police officers patrol the subway.

Fare evasion, a frequent target for critics of the transit authority, is trending down, but also remains a major concern, Mr. Lieber said. In fall 2024, 10 percent of subway riders did not pay the fare, down from 14 percent in the spring. On buses, 45 percent did not pay the fare in the fall, down from 50 percent in the spring.

It is unclear if the federal government will be satisfied with the M.T.A.’s findings, which it will formally submit before the end of the month. Some transit observers have questioned whether the administration has ulterior motives in painting the agency as inept.

Rachael Fauss, a senior policy adviser for Reinvent Albany, a government watchdog group, gave the M.T.A. credit for releasing detailed data about crime in the transit system and congestion pricing. But, she added, “the Trump administration doesn’t care about the facts.”

Federal officials could threaten to delay or withhold funding to gain political leverage in their effort to end congestion pricing, transportation and legal experts said. The M.T.A. is seeking $14 billion from Washington in its next five-year capital budget.

New York’s leaders cannot count on federal funds for the transit system’s capital needs, Ms. Fauss said, and should instead look for local revenue sources, including raising money from suburban areas that have benefited from transit investments.

During Wednesday’s meeting, Mr. Lieber emphasized, “We’re not out to make any enemies; we’re literally in the bridges business.”

Still, one M.T.A. board member could not resist taking a jab at Mr. Duffy.

Neal Zuckerman, the chair of the finance committee, invited the transportation secretary to attend their next meeting, in a post on social media.

“Come on down, Mr. Duffy,” he wrote. “We will protect you from the ‘scary subway.’ You’ll be ok.”