After more than a year of deliberation, the U. S. Environmental Protection Agency has chosen to duck a difficult – and sure to be contested – decision, by asking the U. S. Department of Justice to help it decide how much say Maine Indian tribes should have over what is dumped into waters that flow through tribal land.

While no official agreement has been signed, an EPA official confirmed Wednesday the agency has approved the state’s application to issue federal wastewater discharge permits in the vast majority of Maine. However, the agency deferred a decision on what should be done in “the disputed areas,” said Peyton Fleming, a spokesman for the EPA’s office in Boston.

Those areas include the Penobscot River watershed above Indian Island and some Passamaquoddy lands in Washington County. Twenty-two facilities that need discharge permits are located in those areas. Three hundred facilities are located in the rest of the state, where permitting authority will be granted to the Maine Department of Environmental Protection within the coming days.

Fleming said he did not know how long his agency would consult with the Justice Department before finally deciding what action should be taken regarding the tribal lands. It was also unclear how much, if any, input from the state, tribes and other interested parties would be sought by the Justice Department in its review of the matter.

In late 1999, the state applied to the EPA for permission to issue wastewater discharge permits under the federal Clean Water Act. Forty-four other states already issue the permits on behalf of the EPA.

The Penobscot and Passamaquoddy tribes contested the state’s application, asserting that the federal government should retain permitting authority on waters in Indian territory because the state is too easy on paper companies that discharge wastewater into rivers near their reservations.

In the other states, the federal agency has retained permitting authority in tribal lands, but no other state has an agreement like the 20-year-old Maine Indian Claims Settlement Act.

State officials, as well as a lawyer for several paper companies and Maine towns, contend that the settlement act makes it clear that the tribes are subdivisions of the state and, therefore, do not have the authority to regulate water quality. The tribes, on the other hand, contend that water quality is an “internal tribal matter,” an area the act set aside for the tribes to regulate themselves.

As part of the dispute, three tribal governors were found in contempt of court in November and ordered jailed for not turning over to paper companies documents related to the regulation of water quality. That decision was appealed to the Maine Supreme Judicial Court, sparing the leaders of the Penobscot and Passamaquoddy tribes jail time for the time being.

Reception of the long-awaited decision on the state’s application was lukewarm.

“I wish to heck they had asked the Department of Justice for an opinion eight months ago,” said DEP Commissioner Martha Kirkpatrick.

The state will decide in the next few days whether to grant the EPA an extension to make a decision on what should be done on the tribal lands. The agency was long overdue in issuing its decision on the state’s permit, and the state had denied EPA’s requests for further extensions.

The matter had been held up lately because the federal agency was waiting for biological reports on whether granting permitting authority to the state would harm Atlantic salmon. The fish in eight rivers, including five in Washington County, were put on the federal endangered species list last month. It was determined that salmon would not be harmed by the decision.

“We’re disappointed that EPA can’t make a decision on this,” said Matt Manahan, the Portland lawyer who represents a coalition of paper companies and municipalities that supported the state’s application.

The settlement act makes it clear, he said, that the Department of Environmental Protection has jurisdiction over the whole state. But, he said, the agency has struggled with this and became further mired in confusion when another federal agency – the Department of Interior, which oversees tribal matters – became involved and recommended that the EPA retain permitting authority in tribal lands.

On the other hand, Manahan said it was “encouraging that the EPA is willing to get an objective third-party review” of the matter from the Department of Justice.

Tribal leaders did not return calls seeking comment.