The agency filed a complaint for a permanent injunction with the US Department of Justice, against Mexicali Cheese on 30 January 2012, accusing it of producing cheese under persistant unsanitary conditions that contributed to widespread Listeria monocytogenes contamination.
The FDA is asking a federal court to stop production at the New York-based facility because of a "history of unsanitary conditions."
The complaint has also been extended to two of the facility's officers - Edison Vergara and Claudia Marin.
The New York State Department of Agriculture & Markets (NYSDAM), Division of Milk Control and Dairy Services found similar unsanitary conditions as well as product contamination, the complaint added.
If approved, the injunction would stop manufacture and distribution until operations are brought into compliance with the Federal Food, Drug and Cosmetic Act and FDA food safety regulations.
"FDA filed this complaint to protect the health of consumers," said the agency's associate commissioner for regulatory affairs Dara A. Corrigan.
"Working closely with New York's Department of Agriculture and Markets we took this step to ensure that consumers do not eat potentitally dangerous foods from this company."
A warning letter was sent to the company in October 2009, outlining a number of serious violations that had been noted during an inspection.
The letter followed the recall of Queso Cotija Cheese, which was issued after a sample taken by the NYSDAM was found to be contaminated with high levels of Staphylococcus aureus.
An FDA inspection of the company's New York cheese processing facilities discovered the presence of potentially deadly pathogen Listeria monocytogenes in five locations at the plant.
"During our inspection, we documented conditions and practices that may lead to the contamination of your products with pathogens such as L. monocytogenes and maybe conducive to pathogen growth in your products," the letter said.
"On September 8, 2010, FDA investigators visited you to relay the analytical findings of L. monocytogenes at your firm; during that visit, no change was observed from the violations previously discussed with you and noted on the form FDA483 issued on August 17, 2010," it added.