State regulators were largely cleared Thursday of accusations of "procedural irregularities" while issuing a water quality permit for PolyMet Mining Corp. and the copper-nickel mine it wants to build in northeast Minnesota.

In a victory for the mine's supporters and the Minnesota Pollution Control Agency (MPCA), Ramsey County District Court Chief Judge John Guthmann ruled that the MPCA did not deviate from most of its standard practices when it issued the permit.

"The court finds no overarching effort by the MPCA to keep evidence out of the administrative record," Guthmann wrote in a 104-page decision.

The ruling ends an unusual evidentiary hearing that was narrowly focused on the MPCA and how it reviewed and issued the water permit, which is crucial for the controversial mine to go forward.

Mine opponents — a coalition of environmental groups and the Fond du Lac Band of Lake Superior Chippewa — accused the MPCA of destroying notes on important meetings with the U.S. Environmental Protection Agency (EPA), deleting e-mails and suppressing concerns raised about the project by career scientists at the EPA. They also accused the MPCA of destroying important computer records, including wiping the documents from the computer of the former head of the MPCA a month after he left the agency, for example.

In nearly all cases, Guthmann found the MPCA did not deviate from its standards.

"With today's decision, the court renewed its confidence in the MPCA's permitting process for PolyMet," Darin Broton, a spokesman for the MPCA, said in a statement. "While the MPCA always strives to do better, the court overwhelmingly said the agency's permitting procedures were not irregular. The MPCA remains committed to ensuring that its permit processes and decisionmaking are transparent and provide a robust opportunity for public participation."

Guthmann's decision, however, was not a complete exoneration of the MPCA.

The agency improperly deleted e-mails from former MPCA Commissioner John Linc Stine and Assistant Commissioner Shannon Lotthammer, Guthmann ruled.

Those e-mails showed the two negotiating with the EPA to delay the federal agency from submitting comments critical of the project until after a public comment period was over.

The e-mails should have been disclosed as public records, he wrote.

But because mine opponents and the public were able to find those deleted e-mails through EPA records, Guthmann said the MPCA did not commit what is legally known as spoliation: destroying or failing to preserve evidence.

"Although the Court cannot condone what was at best poor training and careless management … there is no spoliation when the documents at issue were not actually destroyed," Guthmann wrote.

"Spoliation sanctions are not designed to punish failed attempts to destroy evidence, whether accidental or intentional."

The MPCA says it followed routine practices in negotiating with the EPA. Lawyers for the MPCA say the public was fully engaged in the process.

Paula Maccabee, a lawyer at Water Legacy, one of the environmental groups in the lawsuit, said it is a "step forward" that the agency was found to have engaged in some irregularities while issuing the permit.

"The bottom line is that the MPCA asked the EPA to withhold its comments on a very important and controversial permit and then destroyed the evidence that it made that request," she said.

Maccabee said she and other groups are still reviewing the ruling and are considering whether to appeal.

PolyMet's water pollution permit, approved in December 2018, was one of the last of the permits required for the Toronto-based mining company to move toward construction of its proposed $1 billion copper-nickel mine on the Iron Range near Babbitt and Hoyt Lakes.

The project, which would be state's first hard-rock mine, has generated fierce discussion for years.

Mine supporters say the benefits to the depressed Iron Range economy outweigh the environmental risks, which include heavy metals being discharged or leaching into the water-rich landscape.

Environmentalist insist the risks are too great.

The larger question of whether the MPCA's decision to issue the water quality permit to PolyMet was valid still has to be decided.

Environmental groups have appealed the decision to issue the permit, which is now before the Minnesota Court of Appeals.

In August 2019, the Court of Appeals took the unusual step of putting that disputed PolyMet permit on hold, pending the investigation of MPCA "irregularities."

Jon Cherry, PolyMet president and CEO, said in a statement that he looks forward to defending the permit in the Court of Appeals.

"We remain confident the water quality permit meets all applicable standards and will ultimately be upheld by the courts," he said.

Staff writer Jennifer Bjorhus contributed to this report.