The American Lung Association released its State of the Air study using data from 2010 to 2012.
The study gave Sheboygan County the lowest grade in the state. The county had the 25th worst ozone pollution in the country.
Local officials say the data may not accurately reflect air quality in Sheboygan County. The state Department of Natural Resources recently put a new air quality monitor inland from Lake Michigan where the air may be cleaner.
"Are those necessarily accurate numbers? That's unknown. We don't know what the true scientific numbers are because of the position of that reader," Steve Steinpreis, a member of the Sheboygan County Chamber of Commerce's advocacy committee, told Sheboygan Press Media.
Officials in other eastern Wisconsin counties say the pollution comes from Chicago and other urban areas to the south. They say the pollution floats north along the lake and would alter readings from air quality monitors near the shore.
Sheboygan County officials have long said improving the air quality rating is important because failure to meet federal ozone standards could result in lost manufacturing business. Higher costs from air regulations may keep businesses from locating in the area, officials say.
Marathon County and other areas in central and northern Wisconsin had some of the nation's best air quality. The report didn't include the state's smaller counties.
"The air in Wisconsin is certainly cleaner than when we started (the report) 15 years ago," Linda Witucki, executive director of the American Lung Association in Wisconsin, wrote in a news release. "However, the increases in unhealthy days of high ozone tell us we still have work to do."