Even when large farms violate the terms of their permits, it can take years to resolve the problem.

The reason: "stepped enforcement," a progressive form of punishment in which violators are first put on notice that they are out of compliance and given an opportunity to fix the problem.

Failure to do that results in a subsequent "notice of violation," which is followed by one or more meetings with the offender.

The final step is referral to the Department of Justice for prosecution.

Stepped enforcement is not unique to the large farms and is used in other permitting programs.

"It's a very time-consuming process," said Gordon Stevenson, chief of the DNR's runoff management section. "If you are embroiled in enforcement, you are not doing much else. ... So if we can get things resolved by other means, that's what we try to do."

A review of the agency's enforcement actions against the big farms found it sometimes takes two or more years for a case to work its way through the system. In one violation involving illegal agricultural runoff, the incident happened in 1998 and the case wasn't resolved for 10 years, according to DNR records.

In some cases, the farms are violating the law even before they've applied for a permit.

DNR data on new permit applicants show 16 of the farms operating above the 700-cow limit beyond which a permit is required.

"That happens," Stevenson acknowledged. "I know we have farms that are over (size limits) that have not applied for permits."

Still, the agency defends its enforcement record against the big farms.

Stevenson said actions against the farms increased last year because additional staff time was devoted to enforcement. The number of notices of violation issued against factory farms increased from five in 2008 to 30 in 2009. Even so, only three of those enforcement actions resulted in referral to the Department of Justice for prosecution.

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