ST. PAUL — The Minnesota Pollution Control Agency asked the Environmental Protection Agency not to submit written comments on PolyMet’s draft water permit in defiance of the two agencies' established procedures, a former EPA official testified Tuesday in State District Court in Ramsey County.

“That just doesn’t make any sense that we would do that,” Kevin Pierard, the former water permit program chief for EPA Region 5 in Chicago, said. “That just isn’t our practice."

Comments and concerns by the EPA were also read over the phone to the MPCA rather than submitted in writing, a move that kept the comments out of the public record.

PolyMet is trying to build a copper-nickel mine, processing plant and tailings dam near Hoyt Lakes and Babbitt. If built, it would be the first mine of its kind in Minnesota.

Written comments submitted before or during the public comment period are “customary” for the EPA to submit to the MPCA, Pierard said.

Pierard testified via video conference call from Santa Fe, New Mexico, where he now works as the chief of hazardous waste at the New Mexico Environment Department. He sat at a conference table flanked by his personal attorney and three other attorneys representing the MPCA, Fond du Lac Band of Lake Superior Chippewa and PolyMet, respectively.

Paula Maccabee, an attorney for WaterLegacy, one of the environmental groups fighting PolyMet’s permits in court, walked Pierard through numerous draft water permits submitted by the MPCA for projects throughout the state, including several Minnesota iron ore mines and taconite processing facilities, where the EPA made comments on the drafts either before or during the public comment period.

“Most, if not all, of these would have received written comments,” Pierard said as the list of permits were projected on a screen for the courtroom to see.

But, at the urging of the MPCA, the EPA’s comments and concerns were not submitted during the public comment period, despite Pierard and his staff having a fully prepared document detailing numerous concerns. Instead, the comments and concerns were read by EPA staff to the MPCA and over the phone, therefore avoiding the public record.

A coalition made up of environmental groups and Fond du Lac is relating the case against the MPCA and PolyMet in district court.

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, just 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 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.

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. 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.

Pierard said Tuesday there was “hesitation” by the MPCA’s metallic mining sector, then led by Anna Foss, to record correspondence between the state and federal agencies comments in writing, opting for regular conference calls instead of email.

“She (Foss) was much more interested in verbal communication than written communication,” Pierard said.

What is said during a phone call, unlike an email or written letter, would not be included in the official public record. Pierard maintained that not submitting the EPA’s comments before or during the public comment period was unusual and departed from established MPCA-to-EPA procedures.

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.

Tuesday’s hearing did not touch on the mine’s potential to affect the environment, with Judge John Guthmann saying that was for the Court of Appeals to examine. At issue in this district court hearing, he said, is whether the MPCA adhered to administrative protocol in approving the permit.

Guthmann declined early on to exclude any witnesses from testifying.

Saying he would wait for more information to come out in court, Guthmann also deferred judgment on the coalition’s motion to sanction the MPCA for disposing of computer hard drives, notes, emails and other documents related to the permit. The agency has denied that the materials it destroyed were relevant to its official record on the permit and its attorneys reiterated as much Tuesday.

Had Guthmann approved the motion, the court would have essentially said that the materials in question should have been included in the agency’s record.

Throughout her hours-long questioning of Pierard, Maccabee repeatedly asked him if the EPA approached PolyMet’s permitting process the same way that it would have approached any other applicant’s. Attorneys for the MPCA objected, saying that questions about EPA procedures went beyond the scope of the hearing.

They fought to keep the scientific basis of the EPA’s comments from being discussed as well. Guthmann responded by disallowing Maccabee to ask Pierard about the agency’s environmental concerns with the project, saying such questions exceeded the scope of the hearing and would be explored by the Court of Appeals when it revisists the water permit issues.

Pierard is expected to finish testimony Wednesday. John Linc Stine, the former MPCA commissioner who oversaw the agency during the permitting process and issuance, is expected to begin his testimony Wednesday. The coalition is then expected to call former MPCA assistant commissioner Shannon Lotthammer to testify.