Minnesota pollution regulators approved a water permit for the state's first copper-nickel mine over serious reservations raised by their federal counterparts, according to a leaked memo obtained by the Star Tribune.

The 29-page memo was written by Kevin Pierard, chief of the water quality permitting branch in the Chicago office of the U.S. Environmental Protection Agency (EPA). It documents EPA efforts to strengthen water protections in the permit and how those efforts were handled by the EPA and the Minnesota Pollution Control Agency (MPCA).

The memo could play a role in three separate inquiries that are now examining how federal and state regulators handled the critical permit for PolyMet Mining Inc. and its proposed copper mine on Minnesota's Iron Range.

Minnesota environmental advocates have charged that top officials at the EPA in effect suppressed concerns raised by career regulators in the Chicago office, with the result that Minnesota granted PolyMet's permit without addressing all of their objections. Pierard's memo includes a chart of 29 EPA concerns, fewer than 10 of which appear to have been completely resolved.

U.S. Rep. Betty McCollum of Minnesota, who chairs a key House subcommittee on the environment and the interior, described the memo as "shocking documentation," adding: "The EPA scientists who raised the alarm were intentionally overruled in a blatantly politicized and corrupted process."

The memo describes the "refusal" of the Minnesota regulators to include specific numeric limits on heavy metals such as arsenic, cobalt, lead, nickel and mercury that could legally be discharged from the mining operations. Instead, the state opted for less strict standards such as "operating limits" that, Pierard wrote, "may lack a clear regulatory connection to controlling surface water discharges."

Conservationists opposed to copper mining in Minnesota's watery north seized on the memo as fresh evidence of wrongdoing by the regulators.

"This memo shows that EPA's concerns were deeper and broader than what we had realized before," said Paula Maccabee, a lawyer for nonprofit WaterLegacy in St. Paul, which has appealed the water quality permit. "Why would you take something that is a weak ... solution instead of using ... effluent limits that are simple, tough and effective?"

Aaron Klemz, spokesman for the Minnesota Center for Environmental Advocacy, said Pierard's memo shows that Minnesota regulators were not being truthful when they said they had resolved the EPA's concerns.

"This is another piece of evidence of a cover up in the PolyMet permitting process," Klemz said. "It's basically a blueprint for why you should have objected to the permit."

Klemz said Minnesota officials should halt work on the PolyMet project until the issues are resolved.

MPCA spokesman Darin Broton said state regulators are still reviewing the memo and couldn't comment in depth. He disagreed that the memo documents failed efforts to strengthen the permit.

"That's not how I read the memo," Broton said. "I read it as a summary document."

The EPA never officially objected to the permit, he noted. And the last sentence of Pierard's letter in the memo suggests that the EPA supported it: " ... there are legal arguments that can be made to support enforcement of the proposed permit that have been provided to Water Division management and Region 5 Chief of Staff Kurt Thiede."

An EPA spokesman reiterated comments the agency made on the same issue a few weeks ago. Minnesota and the EPA have had a memorandum of understanding in place for years, he said, and under it the EPA can provide its input in various ways. The water permit was "changed to reflect many of EPA's recommendations," he said, and the EPA's actions on the permit "are consistent with the requirements of the Clean Water Act."

The Star Tribune obtained the memo from Nicole Cantello, president of the American Federation of Government Employees Local 704, which represents employees from the EPA Chicago office.

The memo is dated Dec. 18 of last year, two days before the MPCA issued the water quality permit.

Cantello, senior water counsel for water enforcement in the EPA Chicago office, said she doesn't know who sent her the memo. But she said she thinks it was written to document the objections of career EPA scientists to the permit's handling. "He was documenting everything," Cantello said.

Pierard did not return messages requesting comment.

The memo was not included in a batch of e-mails and documents that the EPA Chicago office recently released to the Star Tribune in response to a public records request.

It's the second document about the PolyMet permit that the union has provided, saying it was leaked by an unknown source.

Last month, Cantello provided a leaked e-mail written in March 2018 by Shannon Lotthammer, then an MPCA assistant commissioner, to EPA Region 5 Chief of Staff Kurt Thiede.

In it, Lotthammer asks the EPA not to send its written comments during the public comment period but to hold off until later, citing an agreement the two sides had.

Instead, Pierard read the lengthy comments to MPCA staff over the telephone, several weeks after the public comment period closed.

The result, according to mine opponents, is that critical EPA comments were never formally entered into the public record.

The newly surfaced memo also mentions that arrangement, saying "Region 5 senior management reached an agreement with the MPCA to forgo written comments." It includes an e-mail about the agreement back to Lotthammer from Thiede, who was hired by Trump appointee Cathy Stepp, head of the EPA's Chicago office.

It's not clear whether Pierard is considered senior management.

There are now three separate inquiries into how regulators handled PolyMet's water quality permit, including one by the EPA's inspector general and one by Minnesota's Legislative Auditor. In addition, the Minnesota Court of Appeals decided last month that there was "substantial evidence of procedural irregularities" in how the permit was handled and ordered Ramsey County District Court to investigate.

Late last month, a group of more than two dozen conservation groups around the state, including the Minnesota Environmental Partnership, wrote to Gov. Tim Walz asking him to put a hold on the PolyMet permits pending the investigations.

"We have reached a crossroads not just for the PolyMet copper-sulfide mine, but also for the future of Minnesota's natural resources and the public's faith in government," they wrote.

Walz's policy adviser Charles Sutton responded in an e-mail saying Walz declined but agreed "the court process should go forward."