AUGUSTA, Maine — State officials announced Tuesday that they have sued the U.S. Environmental Protection Agency in a decades-long dispute involving water quality standards on Native American lands.

The conflict centers on whether Maine has jurisdiction over the tribes within their own territories. Though the state argues that it was given that authority by the Maine Indian Settlement Act of 1980, the issue never has been resolved, from the tribes’ perspective. In 2007, the 1st U.S. Circuit Court of Appeals ruled against the Penobscot Nation and Passamaquoddy Tribe in finding that the state has the exclusive right to regulate water quality of rivers that flow through tribal lands.

The Penobscot Nation is located at Indian Island in the Penobscot River near Bangor. The Passamaquoddy also have two reservations that border on water, including Indian Township near Princeton and Pleasant Point near Eastport.

Maine Department of Environmental Protection Commissioner Patricia Aho and Attorney General Janet Mills contend in a suit filed in U.S. District Court in Bangor on Monday that the federal EPA infringed on the state’s rights by approving Maine’s water standards everywhere except on Indian territories, saying essentially that Maine does not have jurisdiction. That creates uncertainty in some areas about which water quality standards apply.

“This is not a problem caused by the state, Maine’s Indian tribes or anyone else in Maine,” said Aho in a written statement. “It is a failure on the part of the EPA to fulfill its legal duties under the Clean Water Act, pure and simple.”

According to Aho and Mills, the state has been asking the EPA for a ruling for more than a year and, in the absence of an answer, there may be some waterways in Maine that are governed by conflicting state and federal standards.

“The EPA appears to be suggesting that the same river might be subject to different environmental standards, which makes no sense,” said Mills. “Where those stretches are and what the standards may be are anyone’s guess. Maine’s water quality standards, in the tradition of Sen. Edmund Muskie and Sen. George Mitchell, are some of the best in the nation.”

Calls for comment from the EPA on Wednesday were not returned.

Tim Feeley, spokesman for the attorney general’s office, said which water standards apply is crucially important in the process of issuing waste discharge and other permits as well as in enforcement actions, which effect towns and industrial facilities along waterways that flow through tribal lands.

“If anyone thinks no rules apply and we try to bring an enforcement action, it becomes pretty difficult,” said Feeley. “The federal court has said the state of Maine has statewide jurisdiction on this issue and we can’t understand why the EPA continues to make these claims.”

The federal 1st Circuit Court of Appeals ruled in 2007 that Maine’s environmental regulatory jurisdiction applies uniformly throughout Maine, including waters within Maine Indian territories, according to Mills.

“The overall message from the courts is that the Settlement Acts are what prescribe the relationship between the state and the tribes, not general Indian law,” Mills told the Legislature’s Judiciary Committee last year in her biennial update on tribal matters.

Tribal Rep. Henry John Bear of the Houlton Band of Maliseet Indians said Tuesday that water quality is just one of many areas of conflict that stem from the dispute around tribal sovereignty.

“This is an issue that keeps coming back,” he said. “What we need are politically sovereign entities that are duly elected by their own tribal members.”

Officials with the Penobscot Nation and Passamaquoddy Tribe either couldn’t be reached Tuesday or weren’t willing to comment publicly on the suit.

Christopher Cousins has worked as a journalist in Maine for more than 15 years and covered state government for numerous media organizations before joining the Bangor Daily News in 2009.