BANGOR, Maine — The state Friday filed an amended complaint in U.S. District Court in its lawsuit against the U.S. Environmental Protection Agency over water quality in tribal waters.

The changes to the complaint, the first version of which was filed last year, are the result of an order issued in February by the federal agency that, according to the state, created a double standard for water quality in Maine — one for tribal waters and another for the rest of the state.

In the decision, the EPA asserts that Maine’s water quality protections, when applied to unspecified tribal waters, must be based on factors such as fish consumption rates and risk levels that are different from those already approved by EPA that are used for the entire state, the Maine attorney general’s office said in a press release.

“This differential treatment violates both the comprehensive 1980 Maine Indian Claims Settlement Acts and the Clean Water Act,” the release said. “Under the Settlement Acts, all Mainers and Maine waters are treated the same for environmental purposes. Maine’s stringent water standards uniformly protect all Maine citizens, including members of Maine’s tribes.”

Wyn Hornbuckle, a spokesperson for the U.S. Department of Justice, which is defending the EPA, declined Friday to comment on the new complaint.

The complaint alleges that the EPA to is trying to force Maine, Washington and Idaho “to adopt the higher end of EPA’s criteria recommendations.” These actions appear to stem from a late 2014 policy directive made at EPA’s national level “regarding the role of tribal treaty rights in the context of EPA’s activities.”

The policy was developed outside the context of Maine’s unique Indian Settlement Acts and appears to encourage the EPA to implement and “enhance protection of tribal treaty rights and treaty-covered resources when [EPA has the] discretion to do so,” the complaint alleged.

It was through the discovery process in a separate pending federal lawsuit in which the Penobscot Nation sued the state over who can police the river that the state discovered the EPA has been carrying on secret correspondence with tribal leaders since at least 1999, the new complaint alleges.

“[The agency] has gone so far as to sign a written ‘confidentiality agreement,’ promising to use EPA’s ‘best efforts to protect all such communications, including those that predate this agreement that are requested under the Freedom of Information Act,’” the press release said.

“These secret negotiations and EPA’s new double standard fly in the face of a major 2007 decision by the First U.S. Circuit Court of Appeals, which affirmed the state’s right to apply the environmental protections inspired by Senator Edmund S. Muskie and Senator George Mitchell, regardless of the ownership of a specific property or the shores of a specific waterway,” the release said.

That decision upheld one of the rights and responsibilities of state government under the 1980 settlement acts to regulate the environmental quality of waters in Maine. The federal government did not appeal that decision to the U.S. Court.

“The [Clean Water Act] has deep roots within the state of Maine, as Maine’s Senator Edmund Muskie was one of the [act’s] chief architects,” the new complaint said. “Consistent with this legacy, Maine takes seriously its responsibility and commitment to uniformly protect Maine’s water quality on behalf of all citizens throughout the state of Maine, including members of Maine’s Indian tribes.”

The EPA must reply to the new complaint by Dec. 11.