Complaints about a troubled manure-processing plant near Waunakee have been referred to the state Department of Justice for enforcement action, officials said Tuesday.

The Clear Horizons LLC facility was cited in connection with three spills totaling 400,000 gallons of manure, failing to remove enough lake-fouling phosphorus from the dairy animal waste before it is spread on farm fields and violating monitoring requirements, the state Department of Natural Resources said in a letter to the company.

DOJ lawyers can go to court to seek fines under state law.

On Aug. 6, an explosion and fire destroyed the roof of one of the facility’s three 1.25-million-gallon manure digesters, but the DNR didn’t allege any violations related to the accident, said Bob Manwell, DNR spokesman.

The fire-damaged unit remained out of commission but the other two were working, a company executive said Tuesday.

“We are pretty confident in the steps we’ve taken to make sure the facility is in full compliance,” said Jim Ditter, CEO of Clear Horizons owner PPC Partners of Milwaukee.

Ditter said Clear Horizons has “turned the corner,” but he said that because of the referral to DOJ he wouldn’t describe any measures the company has taken to improve processes.

The DOJ’s environmental protection unit is reviewing the case to determine a course of action, spokeswoman Dana Brueck said.

The biodigester generates electricity by burning methane gas from manure piped in from three nearby dairy farms. The facility is designed to remove at least 60 percent of the phosphorus from the material before it is returned to the farmers and spread on fields.

Agricultural runoff of the nutrient is a major contributor to weeds, algae, odors and bacteria in lakes.

Clear Horizon’s woes began to emerge on Nov. 24 when a pipe burst and 380,000 gallons of manure poured from a digester. Some of the pollutant flowed more than a mile to a creek that feeds Lake Mendota. No major pollution was detected in the water, county officials have said. An additional 77,000 gallons was released in spills in January and March.

The November release plugged a storm water filtration basin designed to prevent runoff and erosion. Meanwhile, pipeline blockages have forced digester shutdowns that meant hundreds of thousands of gallons of animal waste bypassed nutrient reduction treatment, DNR records indicate.

The state could levy fines up to $1,000 a day for violations, or shut the plant down. But officials said in August that discussions with the company focused on plant upgrades.

Clear Horizons built the digesters at 6321 Cuba Valley Road in the town of Vienna in 2010 for $12 million, including government subsidies.

To minimize spills, the company made changes including installation of some new valves and alarms, and it assigned staff to be at the site around the clock, Ditter said in August. The company was considering better phosphorus-reduction equipment, he said.

Ditter said Tuesday that replacement of the burned roof has been delayed because of insurance company demands that the company obtain multiple quotes from contractors.

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Steven Verburg is a reporter for the Wisconsin State Journal covering state politics with a focus on science and the environment as well as military and veterans issues.