Cleaning the New York City subway has always been a dirty job. But when the pandemic hit last spring, it became even more challenging. When Gov. Andrew M. Cuomo ordered that trains be shut down overnight for cleaning, the Metropolitan Transportation Authority turned to contractors to help undertake the monumental task of scouring the trains in the nation’s largest transit system.

The thousands of workers the contractors hired — largely low-income immigrants from Latin America — were envisioned as a stopgap measure, as M.T.A. workers were falling ill and dying of the virus.

Nearly a year later, the workers are still toiling at stations all over the city. Some are paid as little as half as much as the M.T.A. employees who did the same work before the pandemic began, and many without access to health insurance.

Now, as the M.T.A. prepares to welcome more passengers, the workers are pushing back, raising concerns about their safety, salaries and working conditions.

The New York Times interviewed a dozen contract cleaners, including three who in late February met with Patrick J. Foye, the M.T.A.’s chairman and chief executive, to describe their job and share a list of “needs” with transit agency leadership.

Their accounts paint a picture of dismal working conditions and highlight their unequal treatment compared with transit cleaners, who are paid up to $30 an hour and enjoy health insurance and other benefits, uniforms and MetroCards to swipe themselves into the system.

Beatriz Muñoz, 38, cleaned trains for six months last year at the terminus of the Q line at 96th Street in Manhattan. When cars arrived that were closed to passengers because they had been sullied, “we were the ones who had to go in there,” she said. “We would be praying to God that we wouldn’t get sick.”

Their complaints appear to show how the M.T.A.’s contractors have relied on a labor force that has been desperate for work at a time when hundreds of thousands have lost jobs in cleaning, construction and restaurants.

An M.T.A. spokeswoman, Abbey Collins, said the agency was disinfecting the subway with the help of “licensed and reputable outside companies whose performance is monitored regularly.”

Ms. Muñoz was paid $20 an hour. She brought her own mask, gloves and soap to clean her rags, she said.

She and her co-workers were told not to drink beverages on the job so they would not need to use the bathroom. “It was an oven in the summer,” she said. “We had to sneak sips of water.”

When inspectors came, she said, no one said a word. “Truthfully, we were all afraid.”