A federal watchdog agency is broadening its investigation into the handling of a key water pollution permit for PolyMet Mining's proposed Minnesota copper-nickel mine, giving the probe national scope.

Without issuing any findings on the PolyMet case, the Inspector General of the U.S. Environmental Protection Agency (EPA) has launched a nationwide audit of comparable water quality permits. Specifically, it will examine whether the permits adhere to federal law "based, in part," on the Inspector General's examination of PolyMet, which started in June. A memo announcing the move also cited additional hotline complaints that have been lodged since the one in January that launched the PolyMet inquiry.

The agency will fold its PolyMet findings into the national audit, which means it could be many months before anything is released.

The PolyMet permit is now the subject of three separate inquiries — one by the EPA, one by Minnesota's Legislative Auditor and one in Ramsey County court — after Minnesota environmentalists and a memo leaked to the Star Tribune revealed what have been called irregularities in its handling by federal and state regulators.

The expanded audit was announced in a Sept. 5 memo from Kathlene Butler, a director in the EPA Inspector General's Office, to David Ross, the EPA's assistant administrator for water.

"We initiated that work to determine whether the EPA followed appropriate Clean Water Act and NPDES regulations in Region 5 to review the PolyMet permit approved by Minnesota and issued in 2018," Butler wrote in the memo. "We will incorporate the results from our work assessing the PolyMet permit review into this nationwide audit of the EPA's NPDES permit reviews."

The National Pollution Discharge Elimination System (NPDES) regulates pollutants such as mercury and lead that can be discharged from point sources, such as industrial plants, into surface waters such as lakes and streams.

The Minnesota Pollution Control Agency issued an NPDES permit to PolyMet last year over serious reservations by the EPA's Region 5 Office in Chicago, which oversees Minnesota's enforcement of federal pollution laws.

It later came to light that a state regulator asked the federal counterparts not to submit their written comments on the permit during the public comment period. Instead, an EPA official read the agency's significant concerns about the permit to Minnesota regulators over the telephone after the public comment period closed.

Then an anonymous source leaked a lengthy memo written by the head of the EPA's water quality permit unit in the Chicago office. It documented their struggles with Minnesota regulators to assure the PolyMet permit had the highest level of protection for Minnesota waters, and the "refusal" of Minnesota regulators to include federally enforceable numeric limits on heavy metal pollutants that would be discharged from the mine, called WQBELs.

It also included a chart of 29 EPA concerns about the permit, fewer than 10 of which appear to have been completely resolved when the permit was issued.

In August, the Minnesota Court of Appeals took the unusual step of putting the disputed PolyMet permit on hold pending a District Court investigation of "irregularities" during the permitting process.

The latest EPA memo about the expanded audit doesn't say whether investigators found anything wrong with how the EPA's Region 5 office in Chicago, which covers Minnesota, handled the NPDES permit for PolyMet.

The former EPA attorney who lodged the initial hotline complaint in January said he doesn't know what the expansion might indicate about PolyMet, but called the expansion "good news." He said he believes that there were plenty of irregularities with PolyMet's permit and that it's part of a national pattern threatening the protection of the country's surface waters.

"PolyMet was an extreme example of how bad things could get," said Jeffry Fowley, a former water attorney in EPA's Boston office. "The EPA under Trump has not done a single formal objection to any water permit in any state."

Aaron Klemz, a spokesman for the Minnesota Center for Environmental Advocacy, said he thinks the audit expansion signals that federal investigators found something concerning regarding PolyMet and EPA. "If they had found nothing, they would not be expanding the scope of this investigation," Klemz said.

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