New York has long prided itself on its 24-hour subway, one of the world’s few round-the-clock transit systems and a symbol of the city’s relentless energy. But since the coronavirus outbreak began, the subway has reflected the city’s deterioration: Ridership has plummeted by more than 90 percent, thousands of sick workers have hobbled the ability to run service, and the number of homeless people on trains has grown.

On Thursday, Gov. Andrew M. Cuomo and transit officials took the extraordinary step of trying to restore the system by shutting it down from 1 a.m. to 5 a.m., hoping to provide more time for the disinfecting of trains, equipment and stations during the pandemic.

The decision to halt regularly scheduled overnight service for the first time in the Metropolitan Transportation Authority’s history demonstrates the stark steps state officials are taking to preserve a system that is critical to reviving New York’s economy when businesses begin to reopen.

“We’ve never been here before,” said Mr. Cuomo, who instructed the M.T.A. to devise a plan to clean more frequently earlier this week. “This is going to be one of the most aggressive, creative, challenging undertakings that the M.T.A. has done.”

Shutting down the system overnight is crucial for the transit agency to test and explore disinfecting techniques, including ultraviolet lights and antimicrobial agents, M.T.A. officials said. Still, groups representing riders raised concerns about the indefinite timeline for the shutdown, warning that the pandemic should not be used as an excuse to reduce service permanently.

The overnight closure begins on Wednesday, and the M.T.A. said it would provide free, alternative means of transit to essential workers who need to travel during that time.

Public transit in New York City is the only system in the United States, and among the relatively few in the world, that runs 24 hours a day. The system has shut down only twice in the past decade — in 2011 for Hurricane Irene and in 2012 for Hurricane Sandy, both times for days. In 2015, the system halted passenger service but kept equipment trains running in response to a blizzard.

The decision to temporarily end late-night service will affect roughly 11,000 riders who have been using the system between 1 a.m. and 5 a.m. in recent weeks, according to M.T.A. officials.

Beginning next week, the transit agency will roll out a program offering riders who can prove their travel is essential two free trips on for-hire vehicles each night; it will also provide free rides on buses and in dollar vans. Essential workers will also be able to call a hotline to request a ride, M.T.A. officials said.

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‘Let’s Make Sure That We’re Doing Everything We Can,’ Cuomo Says

Gov. Andrew M. Cuomo of New York provided details about how New York City subways and buses will be disinfected each day.

You now have fewer M.T.A. workers, you have fewer N.Y.P.D. workers on the trains and in the stations. We have now a greater need than ever to disinfect the subways, the buses and the stations. You want to honor the essential workers — Thank you, thank you, thank you. We’ll fly airplanes. We’ll have public demonstrations of gratitude. Yeah, even better than that is what you do and how you act. And let’s make sure that we’re doing everything we can. Let’s clean, disinfect those trucks, those buses and trains every 24 hours. I challenged the M.T.A. to come up with a plan. They came up with a plan. They can disinfect all trains and buses every night. It can best be done by stopping train service from 1 a.m. to 5 a.m. every night during the pandemic so they can actually perform this service.

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Gov. Andrew M. Cuomo of New York provided details about how New York City subways and buses will be disinfected each day.CreditCredit…Mike Segar/Reuters

The M.T.A. was expected to release more details on its plan to provide for-hire cars in the coming days. But the cost to the transit agency will likely add to its financial crisis: It anticipates a shortfall of up to $8.5 billion by the end of the year, and it recently requested $3.9 billion in federal aid in addition to a $3.8 billion federal bailout it received in March.

Bus service will continue throughout the night as scheduled, and the agency will add additional buses where needed when late-night subway service is suspended.

“This is an unprecedented time and that calls for unprecedented action to protect the safety, security and health of our system for customers and employees,” Patrick J. Foye, the M.T.A. chairman, said in a statement. “This closure will enable us to more aggressively and efficiently disinfect and clean our trains and buses than we have ever done before and do it every single day.”

The initiative is a joint effort by the M.T.A., the state and the city, and requires cooperation from the New York Police Department to ensure all passengers vacate subway cars and stations when the system closes each night, officials said.

“It took some disruption to say we are going to do something in this pandemic we’ve never done before, but it makes sense,” said Mayor Bill de Blasio, who joined Mr. Cuomo’s briefing by video.

Still, some riders worry that if late-night subway service were suspended for good, it would hamper the return of New York’s 24/7 culture.

“Having a 24-hour public transit system really affects the spirit and what we are as a city,” said Noah Robbins, 29, who lives in the Bushwick section of Brooklyn and works in Manhattan’s West Village. Mr. Robbins grew up in Boston, where most subway trains stop running at 1 a.m.

“It changes the whole character of the city,” he said. “You don’t get the same night life we have here. The economy changes.”

Many transit advocates said they understood the need to figure out how to disinfect the subway, but they expressed concerns for essential workers who rely on it overnight. They urged state officials to outline a specific plan for late-night bus service to fill the gap, and pushed city officials to ramp up social services for the homeless.

“The governor should announce specific milestones that will trigger the resumption of overnight service,” said David Bragdon, executive director of TransitCenter, an advocacy group. “The criteria announced by the M.T.A. today were much too vague. Riders need more assurance that this is a temporary measure.”

Essential workers who are still using the subway also worried that for-hire cars and vans may not be as reliable as their trains, despite the already reduced service schedule.

“The one thing I really depend on now is the subway system, even if trains don’t come as often. I can depend that it’s my mode of transit to and from work,” said Suk-Yee Wong, 49, a pharmacist from Queens who works at NYU Langone Orthopedic Hospital in Manhattan. “Now I’m getting antsy. If I have to cover a night shift or an overnight shift, how would I get there?”

In recent weeks, the homeless population has become more visible on the system, as usual riders abandoned trains and some people sought shelter on the subway rather than at often-crowded shelters, which have been breeding grounds for the virus.

But with pictures of homeless people on the system circulating on social media, many riders and transit workers have raised concerns about hygiene and safety on largely empty trains.

On Wednesday, M.T.A. officials announced new rules meant to address the issue: Large wheeled carts, like shopping or grocery carts, have been banned from the system; riders cannot remain in a station for more than an hour; and they cannot stay on a train or platform after an announcement that a train is being taken out of service, officials said.

“I want to be clear: The status quo has been completely unacceptable,” said Sarah Feinberg, the interim president of New York City Transit, which operates the subway and buses. “It’s my job to make sure everyone who rides our system feels safe and secure, and that our work force feels safe and secure.”