The Justice Department, on behalf of the EPA, sued the meatpacker IBP Inc., accusing it of polluting the air and water surrounding its Dakota City, Neb. plant.
The suit, filed Wednesday in U.S. District Court seeks fines up to $241 million.
The complaint alleges that IBP violated federal clean air and water laws and hazardous waste management regulations at its slaughter and tannery operations.
The company's six uncovered waste lagoons at the site emitted largely uncontrolled amounts of hydrogen sulfide into the air.
IBP also discharged ammonia into the Missouri River in quantities toxic to aquatic life, the Justice Department said in a statement.
"The public cares about clean air and clean water," said Lois Schiffer, assistant attorney general for Environment and Natural Resources. "Companies that take short cuts in controlling pollution threaten our environments. We will hold them accountable."
The Justice Department is asking the court to order IBP to cover or close its waste lagoons, capture emissions from uncontrolled sources, install additional treatment for its discharges to the Missouri River, and take other steps to protect the environment.
"This case presents a pattern of activity for which the common thread is IBP's avoidance of environmental regulation," said Thomas J. Monaghan, United States attorney for the District of Nebraska. "IBP must now be made to come into immediate compliance with all applicable environmental requirements, and should pay appropriate penalties for its past violations."
IBP officials rebutted the charges, saying the suit will benefit no one and will delay further its planned $13 million in improvements.
The Dakota City plant employs about 4,000 people. IBP is the world's largest producer of fresh beef, pork and related products.
IBP planned to break ground this spring on environmental improvements including construction of three covered wastewater lagoons and installation of equipment to clean air released from the tannery, according to an IBP spokesman.