By Alicia Mundy 

WASHINGTON--The Environmental Protection Agency took the first step Friday to restrict, if not prohibit, the development of Pebble Mine, a proposed open-pit copper and gold mine in Alaska that could be one of the world's largest copper sources.

The EPA said the project poses a serious risk to the salmon fisheries and native tribes in the Bristol Bay area. EPA administrator Gina McCarthy, in a media call, said the agency is turning to a little-used authority under the Clean Water Act to protect the fisheries, which produces about half the world's wild sockeye salmon.

The EPA was acting, she said, "to ensure protection for the world's most productive salmon fishery from the risks it faces from what could be one of the largest open pit mines on Earth." Under a provision in the law, the EPA can prevent the mining company from getting a government permit if it has enough data to show serious environmental dangers.

In January the agency released the results of a three-year scientific study of the project. Ms. McCarthy said the study produced "ample reason to believe that the Pebble Mine would likely have significant and irreversible negative impacts" on the Bristol Bay watershed.

The Pebble Limited Partnership, which is leading development of the mining site, said it intends to fight the EPA's move. "We're pretty confident we're going to drive a stake in it," Pebble CEO Tom Collier said in an interview.

The partnership hasn't yet formally applied for a federal permit, he said, adding he believes the EPA "does not have legal authority" to move to block the mine before a permit is issued.

A spokesman for the EPA, Thomas Reynolds, said, "The agency's authority is very clear under the Clean Water Act."

Mr. Collier also criticized the EPA's scientific study, saying its outcome was "predetermined." The company has written the EPA's Inspector General, requesting an investigation into whether there was "collaboration" between environmental groups and EPA officials to "manipulate the review process" and stop the mine.

He said environmental groups have encouraged native tribes to petition the EPA, which triggered the agency's formal review of Pebble Mine's effect on Bristol Bay.

Mr. Reynolds said, "Every single day, the EPA talks with business, industry, and advocacy groups--it's our business to talk with them." Ms. McCarthy stressed the EPA's process on Pebble Mine is only beginning.

The EPA announcement is one more blow to Vancouver-based Northern Dynasty Minerals Ltd. and its roughly $5 billion project. Northern Dynasty has estimated the copper and gold mine deposits could ultimately be worth between $300 and $500 billion.

Last year, in the wake of falling mining commodity prices as well as a campaign by the environmental community against the mine, Northern Dynasty's partner, Anglo American, withdrew from the project. Some international jewelers also said they wouldn't process Pebble minerals.

In December a major investor in Northern Dynasty, the international mining giant Rio Tinto, said it was reviewing its stake in the company. Rio Tinto had received letters from pension fund managers in California and New York City criticizing the mine proposals because of environmental concerns. Rio Tinto is still conducting its review of strategic assets including Northern Dynasty, said a spokesman for Pebble Mine.

Joel Reynolds, Western Director of the Natural Resources Defense Council, praised the EPA's move. "The science is sound, EPA's legal authority is clear, and the people of Bristol Bay have demanded protection. It's time to say no to Pebble Mine," he said.

Write to Alicia Mundy at alicia.mundy@wsj.com

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