The Environmental Protection Agency and the U.S. Department of Justice announced Coffeyville Resources Refining and Marketing agreed to pay a $970,000 penalty for alleged violations of the Clean Air Act.
The company said it would spend $12 million of the next five years to reduce sulfur dioxide and nitrous oxide emissions.
"This settlement puts CRRM on a level playing field with the more than 100 petroleum refineries that have agreed to implement aggressive pollution control measures, thereby reducing the threats posed by harmful emissions to area residents," said Ignacia Moreno, assistant attorney general for the Environment and Natural Resources Division of the Department of Justice.
The refinery in Kansas has the capacity to refine more than 115,000 barrels of crude oil per day into gasoline, diesel fuels and propane.
The EPA said CRRM's pollution control mechanisms would cut harmful emissions by hundreds of tons per year once they're fully implemented.
"Coffeyville Resources remains committed to operating its facilities in a manner that meets or exceeds environmental regulations," said Robert Haugen, executive vice president of refining operations at CVR Energy, the parent company.