SEATTLE — The U.S. Environmental Protection Agency has penalized a large fishing and seafood processing company for multiple violations of the federal Clean Water Act.

American Seafoods Co., based in Seattle, was fined nearly $1 million for the infractions, which included discharging seafood wastewater in protected areas off the Oregon coast.

The company operates a fleet of seven fishing vessels in the Bering Sea and northern Pacific Ocean. It is the world’s largest at-sea processor of Alaska pollock and holds the largest allocation of wild Pacific hake.

“At-sea” processing means the fish are caught and processed aboard the same vessel.

The EPA charged American Seafoods and the owners of five of its vessels with hundreds of violations that took place off the Oregon and Washington coasts. The vessels are the American Dynasty, American Triumph, Northern Eagle, Northern Jaeger and Ocean Rover.

Among them was discharging wastewater in the Heceta and Stonewall banks complex off the Oregon coast near Florence and Newport. Those areas, according to the EPA, already suffer from low oxygen levels that can harm most fish, crabs and marine life. Biological waste can further exacerbate low-oxygen conditions.

Other violations include failing to monitor discharges and missing or inaccurate information in required annual reports.

Ed Kowalski, director of the EPA’s enforcement and compliance assurance division in Seattle, said American Seafoods “demonstrated a clear disregard for the fragile and valuable resources that sustain its business” through illegal discharges and “sloppy” record-keeping.

In a consent agreement with the EPA, the company agreed to pay $999,000 in fines and conduct “corporate-wide, systemic improvements” to ensure permit compliance.

“When issuing a permit, EPA confers the permit holder the responsibility to protect our nation’s resources,” Kowalski said in a statement. “We expect the company-wide, systemic overhaul of its operations will refocus American Seafoods Co. on the true value of its permit, the importance of tracking compliance with the permit, and the resources that permit entrusts it with protecting.”

In an emailed statement, a spokesperson for American Seafoods described the violations as a “paperwork issue.”

The spokesperson said the company cooperated with the EPA since being notified of the allegations in March, providing documentation and meeting with regulators to better understand how the agency interprets data provided by the vessels.

American Seafoods also is working with third-party consultants to ensure permit compliance and has assigned additional staff to ensure its reporting is timely, accurate and complete, according to the spokesman.

”American Seafoods continues to have the highest priority focus on reporting and compliance and looks forward to putting this matter behind us,” the spokesman said.