Minnesota's controversial handling of a critical water permit for the PolyMet Mining copper-nickel project appears to have involved the very highest officials of the state Pollution Control Agency (MPCA), according to newly released documents.

The involvement of the agency's top official adds a new element to an episode that is already under scrutiny by Minnesota's legislative auditor, a Ramsey County judge and the inspector general of the U.S. Environmental Protection Agency (EPA). Minnesota environmentalists have accused top officials at the two agencies of cooperating to suppress concerns raised by federal regulators by reading their comments over the phone rather than including them in the written public record on the permit.

The direct involvement of John Linc Stine, then commissioner of the MPCA, was revealed in e-mails obtained by the St. Paul conservation group WaterLegacy. The group sued the EPA for their release this month and released some of the documents Thursday.

The Star Tribune has also filed a public-records request for the documents, but the EPA hasn't fully responded.

WaterLegacy lawyer Paula Maccabee expressed outrage over the new documents, saying the e-mails show a concerted effort at secrecy in the process of permitting a large project with grave environmental consequences.

"The reasons permits are issued or denied are supposed to be public, in the public record, and there is not supposed to be Freedom of Information Act lawsuits to find out what Minnesota's government did," Maccabee said.

The documents contain an e-mail from Stine to Cathy Stepp, President Donald Trump's appointed head of EPA Region 5 in Chicago, and her chief of staff, Kurt Thiede. In the e-mail, dated March 12, 2018, Stine thanks the two federal regulators for a phone conversation and says his assistant commissioner for water, Shannon Lotthammer, will follow up with Thiede regarding the "Region 5-MPCA agreement I mentioned on our call."

The next day, Lotthammer sent an e-mail to Thiede asking Region 5 not to send written comments on the draft permit during the public comment period and instead follow a 1974 Memorandum of Agreement in which the EPA delegated enforcement authority to Minnesota.

Lotthammer's e-mail first surfaced in June after it was leaked to the union representing career employees of the EPA's Chicago office.

Lotthammer now works at the Minnesota Department of Natural Resources and has declined to discuss the episode.

Stine did not immediately respond to a request for comment on Thursday. But in previous interviews, he has said he did not recall complaining to the EPA office about its comments. The lack of written comments available to the public is not a lack of transparency, he said, it's "just the way everybody does business."

Asked about the new documents, MPCA spokesman Darin Broton said the agency was following familiar protocols and has no authority to instruct a federal agency not to submit comments.

"The e-mail clearly states the MPCA's concern about the timing of the EPA's comments and encourages the EPA to submit comments after the MPCA addresses the public's comments, which is a long-held policy between the two agencies," Broton said.

However, an EPA Region 5 memo obtained by the Star Tribune clearly states that the EPA files comments during public comment periods as part of its regular oversight.

The MPCA ultimately issued the water quality permit for PolyMet's proposed northeastern Minnesota mine at the end of 2018. As WaterLegacy pursued information about the permit process, documents and e-mails continued to surface suggesting that the EPA Region 5 office had grave concerns about the proposed permit, including a lack of stringent, measurable limits for pollutants such as lead and mercury in the mine's wastewater.

The Minnesota State Court of Appeals has stayed the water permit pending the outcome of a yet to be scheduled hearing on alleged "irregularities" in the process.