In another reversal of Obama administration policy, the Environmental Protection Agency announced Friday that it had settled a lawsuit over a mine near Alaska’s Bristol Bay, one of the world’s most productive salmon fisheries.

Pebble Limited Partnership, the site’s developer, sued the agency, claiming that the Obama administration had colluded with the project’s opponents to block copper, gold and silver extraction at the site. An E.P.A. review found no evidence of such collusion.

Friday’s settlement allows the company to file a new application for a permit, which it has said it will do. That effectively undercuts the E.P.A.’s previous determinations, based on years of scientific study, that the proposed mine on state land would be a risk to the long-term health of the fishery and wider ecosystem.

In a call with shareholders on Friday, executives for Pebble Limited Partnership and Northern Dynasty Minerals, the partnership’s parent company, thanked Scott Pruitt, the administrator of the E.P.A., for the favorable treatment under the new administration and “his commitment to the rule of law.”