PORTLAND — One of Maine’s largest seafood processors is shut down for a final inspection while a federal judge reviews a legal agreement to settle concerns about food safety violations in the company’s plants.

The proposed consent decree was filed Tuesday by U.S. Attorney Thomas E. Delahanty against Portland Shellfish Co., citing unsanitary conditions at its processing plants in Portland and South Portland.

The filing followed four recalls stemming from two episodes of contamination of cooked lobster meat since 2008. The meat was found to be contaminated by the bacteria Listeria monocytogenese, which causes listeriosis, a potentially fatal disease for high-risk groups such as pregnant women, newborns, the elderly and people with compromised immune systems. Symptoms include headache, fever and vomiting.

In the proposed consent decree, Portland Shellfish agrees to fully comply with conditions set by the U.S. Food and Drug Administration to ensure that the company follows food safety regulations.

Jeffrey Holden, president and founder of Portland Shellfish, said Wednesday that the 35-year-old company has made sanitation improvements at its crab processing facility on Dartmouth Street in South Portland and its lobster and shrimp facility on Waldron Way in Portland.

The plants ceased operating Tuesday, but Holden said he expects them to resume operations soon.

Portland Shellfish processes about 13 million pounds of raw lobster, shrimp and crab a year. It ships more than 5 million pounds of finished products to commercial customers who distribute them to restaurants and other retailers nationwide.

Holden said his company has agreed to the terms of the consent decree with the FDA to settle the agency’s concerns. He said the plants, which employ 150 workers, will reopen as soon as he receives word from the FDA that they may do so.

Holden said he is unaware of any illnesses caused by the recalled products.

Doug Karas, an FDA spokesman in Washington, D.C., declined to comment on any agreement between the agency and Portland Shellfish.

Documents filed in U.S. District Court in Portland charge the company with repeated violations of federal food safety laws, first identified by FDA investigators in March 2001, and with failing to create and follow a food safety oversight plan.

Portland Shellfish issued voluntary recalls of lobster meat processed at its Waldron Way plant in October 2008 and June 2010, after the meat tested positive for the Listeria bacteria. An ensuing FDA inspection revealed bacteria in the plant.

Court records cite unsanitary conditions documented by FDA investigators last year at the South Portland plant. They include rust buildup on a crab saw blade, white residue on a conveyor belt, crabs lying on the processing room floor, condensation dripping from a pipe directly above cooked crab meat, water leaking from the ceiling, and an employee walking through a puddle and splashing floor water onto cooked crabs.

Portland Shellfish Co. is also inspected by the Maine Department of Agriculture, which found conditions similar to those cited by the FDA at the South Portland plant this year.

Steve Giguere, program manager for the agriculture department’s division of quality assurance and regulations, said the U.S. attorney rarely takes court action against a Maine food processor.

“The FDA doesn’t take this kind of action lightly,” he said.

Holden invited reporters to tour his plant in Portland on Tuesday. Workers were busy installing new equipment and cleaning the 21,000-square-foot facility, in an industrial area off Riverside Street.

Holden said he invested more than $750,000 last year on new equipment designed to make the production process cleaner and more efficient. He also hired two permanent quality assurance experts.

“We are very serious. It is the most important thing we have going, food safety,” Holden said.

Foot baths have been placed at entrances throughout the building, and a new $250,000 forced steam convection oven ensures that lobsters are fully cooked.

To kill bacteria in the water that’s used in the production process, Holden said, the company bought a new disinfecting system that uses ozone, a more effective agent than chlorine.

Holden said the company has worked diligently to meet all of the FDA’s conditions and has gone beyond what federal regulators require. He said that since June, all of Portland Shellfish Co.’s lobster meat has tested negative for the Listeria bacteria.

He also said he has received no complaints from customers or lost any business.

“Business is up this year in every category,” he said.

The consent decree would require Portland Shellfish to pay all FDA costs, such as inspectors’ time and mileage, associated with ensuring that the company remains in compliance. Portland Shellfish could petition the court to dissolve the agreement in five years.

Staff Writer Dennis Hoey contributed to this report.

Staff Writer Beth Quimby can be contacted at 791-6363 or at: bquimby@pressherald.com