The Minnesota Pollution Control Agency did not violate its own policy or break the law when it requested federal regulators refrain from commenting on an essential water permit for PolyMet, the project aiming to be Minnesota's first copper-nickel mine, a judge said Thursday.

A coalition of environmental groups and the Fond du Lac Band of Lake Superior Chippewa argued the MPCA urged the Environmental Protection Agency to wait on commenting on a PolyMet draft permit until the public comment period ended and to read comments over the phone instead of putting them in writing (and the public record), which represented "procedural irregularities" and an effort by the MPCA to suppress EPA concerns on PolyMet's National Pollutant Discharge Elimination System, or NPDES, permit.

But on Thursday afternoon, Judge John H. Guthmann filed a 104-page findings of fact, conclusions of law and order in State District Court in St. Paul that countered those claims and sent the case back to the Minnesota Court of Appeals.

"The MPCA effort to convince the EPA to delay issuing written comments about the NorthMet NPDES draft permit was not an irregularity in procedure," Guthmann wrote. "There is no statute, rule, regulation, or other formally adopted policy or procedure that prohibits the MPCA from asking the EPA to delay an optional course of action."

But Guthmann acknowledged the MPCA kept EPA comments from the public view to deter bad press, even if no law or rule barred the agency from it.

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“The MPCA knew it was required to respond to all written EPA comments, its responses would be public, and the public would find out what the EPA’s specific concerns about the permit were from the comments and responses” Guthmann wrote. “The MPCA had other legitimate reasons for seeking an EPA delay in submitting comments. However, the MPCA’s primary motivation was its belief that there would be less negative press about the NorthMet Project if EPA comments were delayed until after public comments and verbally expressed EPA concerns were incorporated into the draft permit.”

On Thursday evening, environmental groups still characterized the judge's order as a partial win.

"Judge Guthmann has actually agreed with us on the basic facts that evidence was hidden from the public and that emails were destroyed ... he had a very narrow ruling in terms of what that meant on the law, but he confirmed the facts," said JT Haines, a spokesperson for the Minnesota Center for Environmental Advocacy.

Pete Marshall, spokesperson for the Friends of the Boundary Waters Wilderness, and Paula Maccabee, counsel and advocacy director of WaterLegacy, echoed Haines' statement and said their groups planned on appealing.

The groups all pointed to a section in the findings of fact that explained the MPCA had "destroyed" its emails urging the EPA to delay its comments.

"The act of destroying (the emails) was an irregularity in procedure not shown in the record," Guthmann wrote.

Maccabee called those emails "smoking guns" as it shows the MPCA trying to stifle concerns the EPA had on the permit.

But in his order later in the document, Guthmann said because "the documents were located elsewhere, they are available for inclusion in the administrative record."

"The MPCA did not engage in a systematic effort to keep evidence out of the administrative record," Guthmann wrote.

Noting the exception of those emails and a one set of notes taken by the MPCA's permit writer that were recycled after a phone call with the EPA, Guthmann wrote: "(The coalition) failed to satisfy their burden of proving that the agency destroyed documents or other evidence that should have been placed in the administrative record or should have been available for inclusion in the Transfer Hearing record."

In an emailed statement, MPCA spokesperson Darin Broton said Thursday's decision meant "the court renewed its confidence in the MPCA’s permitting process for PolyMet."

"While the MPCA always strives to do better, the court overwhelmingly said the agency’s permitting procedures were not irregular," Broton said. "The MPCA remains committed to ensuring that its permit processes and decision-making are transparent and provide a robust opportunity for public participation."

PolyMet is trying to build a copper-nickel mine, processing plant and tailings dam near Hoyt Lakes and Babbitt. In a news release Thursday evening, characterized the judge's order as a win.

“We are pleased with the district court’s ruling and look forward to defending the challenge to the water permit currently pending in the court of appeals,” said Jon Cherry, chairman, president and CEO of PolyMet. “We remain confident the water quality permit meets all applicable standards and will ultimately be upheld by the courts.”

The MPCA and EPA’s review of the permit was transferred to district court last year by the Minnesota Court of Appeals, which, in a separate case, reversed PolyMet’s dam safety permits and permit to mine back to the Minnesota Department of Natural Resources and ordered a contested-case hearing.

An email leaked in June 2020 by the union representing EPA employees in the region appeared to show former MPCA assistant commissioner Shannon Lotthammer asking Kurt Thiede, then the EPA’s regional chief of staff, to keep the agency from commenting on a draft of the permit until after the conclusion of its public comment period. The union and opponents of the mine argue the email showed the MPCA suppressed the EPA's concerns.

During a weeklong hearing in January, Kevin Pierard, the former water permit program chief for EPA Region 5 in Chicago, said the MPCA asking the EPA not to submit written comments before or during the public comment period was unusual and a departure of the established MPCA-to-EPA procedures.

"That just doesn't make any sense that we would do that," Pierard said. "That just isn't our practice."

The agencies instead shared comments over a phone call, Pierard said. What is said during a phone call, unlike an email or written letter, would not be included in the official public record.

The MPCA maintains it was following a memorandum of agreement between itself and the EPA that, among other things, lays out the procedure for commenting on permits.

Later in the hearing, John Linc Stine, the MPCA commissioner at the time, said he wasn't aware of another major instance in which the MPCA explicitly asked the EPA to refrain from commenting on a permit until after public comment ended.

But he denied that he complained to two regional officials with the EPA about the timing of the comments to keep them out of the public record.

"I continue to say that I did not complain," he said.

The MPCA’s handling of the comments remains under investigation not only by the courts by the EPA’s Office of Inspector General and the Minnesota Office of the Legislative Auditor as well.

The release of Lotthammer's email came less than one week after the EPA released documents showing the agency was concerned a draft permit would not meet the Clean Water Act standards unless the MPCA made substantial changes to the permit and the EPA’s office of inspector general said it would audit the agency’s PolyMet permitting procedures.

PolyMet faces numerous other court cases and challenges to its permits.

This story was updated several times with reaction from involved parties and additional information from the judge's order. The final version was published at 7:13 p.m. Sept. 3. The initial version was posted at 4:31 p.m. Sept. 3.