ST. PAUL — The Minnesota Pollution Control Agency said Tuesday it has taken the unusual step of denying a permit for a large hog farm proposed for Fillmore County in southeastern Minnesota because of the threat of adding to groundwater nitrate pollution in the geologically porous region.

MPCA Commissioner John Linc Stine said at a news conference that he denied the general permit for Waukon, Iowa-based Catalpa Ag’s proposed 4,890-sow facility near Mabel because of the threat to public health. The piglet-producing operation would have generated over 7 million gallons of manure annually that would be spread on farm fields for fertilizer.

Groundwater nitrate levels in 19 of the county’s 24 townships already exceed the state’s safe drinking water standard of 10 parts per million, he said.

“We typically do not deny feedlot applications,” Stine said, noting that thousands of feedlots now operate across the state.

Denying the permit means there’s no need to decide on requests by project opponents for a full environmental impact statement, Stine said. He recommended that the state Environmental Quality Board authorize a broader, state-funded study of groundwater pollution in the region instead.

Stine also said Catalpa still has the option of starting over and applying for a customized permit known as an individual permit.

But he said any future application process would require a more rigorous analysis, with another chance for the public to comment. He said the protections provided by the general permit that Catalpa sought would be insufficient.

Catalpa is owned by the Al Hein farm family near Rochester. Hein said they will now re-apply for the individual permit and cooperate with the proposed study as they seek to diversify beyond crop farming and provide farmers in the area with a cheaper, more natural source of fertilizer.

“I was a little disappointed that we didn’t get the permit but it doesn’t really kill the project,” Hein said.

Two public meetings about the project drew more than 700 people, including opponents concerned about groundwater quality and odors.

Minnesota Health Commissioner Jan Malcom issued a statement supporting Stine’s decision.

“Nitrates in drinking water can cause blue baby syndrome in bottle-fed infants less than 6 months old and may increase the risk of harm for people with certain health conditions,” she said. “Preventing additional problems is far less costly than leaving it to additional private well owners or communities to treat their water for nitrates.”