A high-end Hancock seafood company has been shut down for repeated unsanitary conditions and food safety violations, including manufacturing in the presence of rodent excrement, according to the U.S. Department of Justice.

U.S. District Judge Jon D. Levy on Friday signed a consent decree of permanent injunction against Mill Stream Corp., which does business as Sullivan Harbor Farm, and its owner, Ira Joel Frantzman.

The action followed more than a decade of warnings to the company by the Food and Drug Administration, which found the company’s smoked fish products were being prepared, packed and held under unsanitary conditions so that the products may have become contaminated with filth or rendered injurious to health, says a complaint filed by the Justice Department in U.S. District Court in Maine.

The company, founded in 1992, has annually made about 75,000 pounds of ready-to-eat smoked fish and fishery products, such as smoked salmon, trout and char, which are sold across the country. Customers include Legal Sea Foods in Boston and Dean & DeLuca of New York. The company’s smoked fish products have received a number of food industry awards.

According to the complaint, an FDA inspection in March and April 2015 identified significant, recurring violations at the business on Route 1, including inadequate plans to control risks of a neurotoxin that can cause botulism.

The FDA also observed rodent “excreta pellets too numerous to count in the area of the facility where smoker trays are cleaned, apparent black mold and water staining on the door frame of the walk-in freezer where fish is stored, an open rack of salmon stored beneath a pipe with frozen condensate build-up, water splashing from the processing floor onto a cutting board and into bins where fish was stored.”

The complaint says that a December 2011 inspection revealed the presence of Listeria monocytogenes in the facility’s environment and on a fish-skinning machine. The company recalled and destroyed the affected products.

The complaint also says that for more than a decade the FDA repeatedly warned the company about violations through regulatory meetings, telephone calls and other measures but the violations continued.

In conjunction with the filing of the complaint, the company has agreed to settle the case and has ceased all manufacturing operations, according to a news release from the Justice Department. The FDA must determine that the company has complied with all safety regulations before it may resume manufacturing.

No one was available at the company Sunday. A message on its website says its smokehouse is closed for training to improve the facility.