Minnesota’s top environmental regulator has denied a permit for a large swine feedlot in southeastern Minnesota, citing concerns about the region’s already-troubled groundwater, though the decision has not quashed the project.

Commissioner John Linc Stine, of the Minnesota Pollution Control Agency (MPCA), said Tuesday he is denying Catalpa Ag’s request for a general permit for its 4,890-hog facility. But the company can still obtain a more rigorous individual permit if it takes additional steps to prevent leakage that would contaminate groundwater.

Stine said he made the decision in the interests of the region, which is sensitive to water contamination because its porous, karst geology can allow surface contaminants to reach the groundwater “within a matter of minutes.”

“There are thousands of feedlots across the state,” Stine said. “This one was in a very sensitive area and did not make sense to me for a general permit.”

Catalpa’s proposed facility wouldn’t be the largest feedlot in the state, but it drew unusual public interest, including hundreds of letters in opposition and two crowded hearings. Concerns ranged from the smell to traffic to the facility’s potential to exacerbate or increase the number of sinkholes in the soggy region.

At least one opponent said she was disappointed in Stine’s announcement because opponents wanted the agency to order an environmental impact statement (EIS), a comprehensive review that would fully identify risks associated with the project near Mabel, Minn. Under Stine’s ruling the site’s owner, Al Hein, can apply for an individual permit without conducting such a study, said Dayna Burtness, a hog farmer from Spring Grove, Minn.

“We’ve been asking for an EIS,” she said. “This feels like a dodge.”

Most of the state’s 1,300 feedlots are covered under general permits, but about 70 have received the more-rigorous individual permits, according to the MPCA.

Reached after Stine’s announcement, Hein said Catalpa will pursue an individual permit. Hein, a majority shareholder of the company, argued that the feedlot will offer ecological benefits. Tanks under the proposed barns would collect up to 9 million gallons of liquid manure, which could be used as organic fertilizer on area fields and reduce the amount of commercial fertilizer in the soil, Hein said.

Hein said he was disappointed to be denied the general permit but said it was a victory to not be ordered to conduct a company-funded EIS. Such reviews are common for large-scale projects, such as the proposed PolyMet copper mine in northern Minnesota, but rare for feedlots.

“In that sense, it was a good thing,” he said. “If we can just alleviate the other concerns [to prevent leakage into the groundwater] then we just move along with the process.”

In lieu of a project-specific EIS, Stine recommended a state-funded study by the Environmental Quality Board of the entire region and its sensitivity to groundwater contamination. Already, 19 of 24 townships in Fillmore County have private wells with nitrate levels above health risk limits, according to a state Department of Agriculture study.

“That fact alone gave me great pause,” the commissioner said. “We know the source of nitrates in drinking water comes from our surface activities.”

Minnesota Health Commissioner Jan Malcolm praised Stine’s decision and supported the call for a regional study, but whether the board will conduct one is unclear. It’s also unclear whether such a study would affect ongoing permit applications for Catalpa or other projects.

If Catalpa applies for an individual permit, then environmentalists would once again call for an EIS and everyone would be back where they started, said Bobby King of the Land Stewardship Project, a nonprofit advocacy group that opposes the feedlot.

“There would be only two possible outcomes of an EIS,” King predicted. “ ‘This can’t be done safely here,’ or, ‘This project needs to be substantially changed.’ ”