The review of a draft water permit for PolyMet's controversial proposed copper-nickel mine near Hoyt Lakes, the first of its kind to be fully permitted in Minnesota, is under more scrutiny.

The Minnesota Court of Appeals in an order Tuesday said a hearing should be held on "procedural irregularities" in the Environmental Protection Agency's review of a draft water permit later granted by the Minnesota Pollution Control Agency to PolyMet.

Additionally, the Office of Legislative Auditor, a nonpartisan office of the Minnesota legislative branch, will also probe the permit review process after a lawmaker requested an investigation Monday.

The announcements come after documents released this month showed the Environmental Protection Agency was concerned a draft of the water permit would not meet the Clean Water Act standards unless the Minnesota Pollution Control Agency made substantial changes and a leaked email showed an MPCA official requested the EPA not comment on the draft permit until public comment ended.

Opponents of PolyMet say those documents prove the MPCA stifled EPA concerns on a draft of the permit, which the MPCA later granted to PolyMet.

In its order, the Court of Appeals backed a motion by WaterLegacy — an environmental law group opposed to PolyMet that appealed the company's water permit — arguing the Court of Appeals should pause its appeal process so a district court can weigh whether the recently released documents should be included in the record.

"We conclude that (WaterLegacy) has provided substantial evidence of procedural irregularities not shown in the administrative record, and thus that it is appropriate to transfer this matter to district court for a hearing and determination of the alleged irregularities," Minnesota Court of Appeals Chief Judge Edward Cleary wrote in the order Monday.

On Monday, Rep. Rick Hansen, DFL-South St. Paul, called on the Office of Legislative Auditor to conduct an "independent, nonpartisan, third party investigation into the (MPCA) to ensure the public’s trust in our state’s ability to protect water quality and the environment."

Legislative auditor Jim Nobles told Minnesota Public Radio News Tuesday that he agreed to Hansen's request "because I think it raises issues and concerns about the processes of government on a very important issue. The PolyMet mine process for approving the permits has been longstanding and very controversial. And so it's another piece of the controversy that I think needs to be addressed, and as expeditiously as possible."

MPCA spokesperson Darin Broton told the News Tribune Tuesday that the agency stands by its permit decision, but recognizes the commenting process between the MPCA and EPA has raised concerns.

MPCA Commissioner Laura Bishop "wants to make sure permitting process more transparent and clear for all parties on how and when those comments are going to be received to, again, make sure they are part of the public record."

The MPCA's handling of EPA concerns over the permit have slowly come to light after Jeffry Fowley, a retired EPA attorney, said multiple people raised concerns with him that the EPA’s concerns and comments on PolyMet’s draft permit were told to the MPCA over the phone instead of in writing, leaving their concerns out of the public record.

The EPA’s office of inspector general has also announced it would audit the agency’s PolyMet permitting procedures.

Minnesota Public Radio News contributed to this report.