Tesoro Corp. and Par Hawaii Refining were found to be in violation of the Clean Air Act. They have agreed to a $425 million settlement with the Department of Justice and Environmental Protection Agency.

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Tesoro, which operates a refinery in Anacortes, and another company reached a $425 million settlement with federal agencies to resolve allegations of violations of the federal Clean Air Act in six states.

Tesoro and Par Hawaii Refining have agreed to pay roughly $400 million toward better controlling emissions under a civil settlement announced Monday by the U.S. Department of Justice and the Environmental Protection Agency.

Tesoro also will pay $10.4 million in penalties and put money toward other projects as a part of the settlement that resulted from the 2008 discovery of violations of the Clean Air Act in the Anacortes refinery.

All but $75 million of the total already has been spent, with the rest to go for improvements over the next several years, according to a Tesoro spokesperson.

The DOJ and EPA believe that the companies’ refineries exposed residents of Anacortes, along with five other Western locations, to substances in the air that might result in heightened cancer risks and aggravated asthma problems in children.

The changes Tesoro agreed to are expected to cut down heavily on the toxic air pollutants the refineries have been releasing, according to the agencies.

“The Department of Justice and the EPA have been working for years to get this settlement,” Mark Asmundson, executive director of the Northwest Clean Air Agency, said at a news conference to announce the settlement. “Oftentimes, people say our government isn’t doing anything right; this is a perfect example of government working for the people.”

Asmundson was joined at the news conference at the Seattle Coast Guard base by Annette Hayes, U.S. attorney for the Western District of Washington; Dennis McLerran, director for EPA Region 10; and John Cruden, assistant attorney general in the Justice Department’s Environmental and Natural Resource Division.

“This is the home of United States Coast Guard men and women, who are most directly affected by many of the impacts of climate change, rising sea levels, ocean warming and acidification … and changes of the frequency and intensity of severe weather events,” Hayes said. “So, I think this a very appropriate place to announce a major settlement that will reduce greenhouse-gas emissions across six Western states and beyond.”

At the Anacortes refinery, some of the alleged violations date back as far 2001, according to the Justice Department complaint filed as part of the settlement. They include inadequate leak detection and the threshold in which a leaking pump is required to be repaired. Tesoro also was found to be violating flaring regulations, resulting in an excessive amount of air pollution.

Tesoro operations at Anacortes have repeatedly come under scrutiny in years past.

An April 2010 explosion at the refinery killed seven people. In 2014, a federal Chemical Safety Board investigation found that the disaster occurred, in part, due to poor inspection procedures, the failure to use safe equipment, and employees placed in unnecessarily dangerous situations.

Earlier this year, the EPA fined the company nearly $720,000 for safety violations found several years prior, unrelated to the settlement.

For Tesoro, the settlement comes as the company and a joint venture partner seek state approval of a major new crude-by-rail terminal in Vancouver, Wash., to bring Bakken Shale crude to West Coast refineries. That terminal has met fierce opposition, with opponents citing safety and environmental concerns.

The $10.4 million penalty is the highest of its kind, according to Cruden, who credited Tesoro for taking responsibility instead of seeking legal action.

“It’s good because, otherwise, if we were litigating it, nothing happens, nothing happens to the environment,” he said. “We would be years from now before we would be able to resolve that case.”