The U.S. Food and Drug Administration is asking a federal court to prevent a New York cheese manufacturer from operating because of a history of unsanitary conditions and producing cheese in a facility contaminated with Listeria monocytogenes.

According to a complaint for permanent injunction filed by the U.S. Department of Justice, Mexicali Cheese of Woodhaven, N.Y., and two of its officers, Edinson Vergara and Claudia Marin, produced cheese under persistent unsanitary conditions that contributed to widespread Listeria contamination in Mexicali Cheese’s facility.

In addition, the complaint, filed January 30 in the U.S. District Court for the Eastern District of New York, says that the New York State Department of Agriculture & Markets, Division of Milk Control and Dairy Services found similar unsanitary conditions in addition to product contamination.

Inspections over the last three years, which were set off by the finding of staphylococcal bacteria in a cheese sample in 2009, have turned up a long list of violations, including equipment that was covered in harmful bacteria; flies, maggots and mold in production areas; stagnant pools of dirty water on the floor; and rodent excrement in the supply rooms, the suit said.

Telephone calls to the company were not answered on Tuesday.

Mexicali Cheese Corporation, based at 91-52 87th Street, primarily distributes Mexican-style cheese to grocers in New York, New Jersey and Connecticut.

Inspectors from the New York State Department of Agriculture and Markets have visited the factory more than 30 times since 2009, according to the report, and F.D.A. inspectors have also made visits. Inspectors said they found listeria on a dolly used to transport cheese throughout the plant, on the aprons of food handlers and in a pool of liquid in a storage area.

During one inspection, an employee was seen putting cheese in his mouth, then continuing to work without changing his gloves. The suit also said that “employee food handlers were observed wiping perspiration from their faces with their forearms while wearing disposable gloves that only covered the hands up to the wrists, leaving bare forearms exposed and in direct contact with the ready-to-eat cheese being processed.”

In 2010, the F.D.A. found a batch of Mexicali’s “Queso Cotija” to be contaminated with staphylococcal bacteria, and the company voluntarily recalled the product. But later that year, and again in 2011, when inspectors found there was listeria in the facilities, the company would not recall the nearly 300 pounds of cheese that had been made on the day the samples were taken.

When pressed by inspectors, Ms. Marin said on both occasions that the cheese had most likely already been consumed, and that no one had reported any illness related to the product. According to the complaint, Mr. Vergara and Ms. Marin agreed that improvements to the plant were necessary, but in follow-up visits, inspectors noted that no changes had been made.

Mexicali Cheese makes and distributes a variety of soft Mexican cheeses to grocery stores and supermarkets in New York, New Jersey and Connecticut. Mexicali Cheese’s products include queso fresco [fresh cheese], queso oaxaca [Oaxacan cheese] and queso para freir [cheese for frying].

If entered by the court, the injunction would stop the company and its officers from manufacturing and distributing food until they can bring their operations into full compliance with the Federal Food, Drug, and Cosmetic Act and FDA food safety regulations.