It was the two-headed baby trout that got everyone’s attention.

Photographs of variously mutated brown trout were relegated to an appendix of a scientific study commissioned by the J. R. Simplot Company, whose mining operations have polluted nearby creeks in southern Idaho. The trout were the offspring of local fish caught in the wild that had been spawned in the laboratory. Some had two heads; others had facial, fin and egg deformities.

Yet the company’s report concluded that it would be safe to allow selenium — a metal byproduct of mining that is toxic to fish and birds — to remain in area creeks at higher levels than are now permitted under regulatory guidelines. The company is seeking a judgment to that effect from the Environmental Protection Agency. After receiving a draft report that ran hundreds of pages, an E.P.A. review described the research as “comprehensive” and seemed open to its findings, which supported the selenium variance for Simplot’s Smoky Canyon mine.

But when other federal scientists and some environmentalists learned of the two-headed brown trout, they raised a ruckus, which resulted in further scientific review that found the company’s research wanting.

Now, several federal agencies, an array of environmental groups and one of the nation’s largest private companies are at odds over selenium contamination from the Idaho phosphate mine, the integrity of the company’s research, and what its effect will be on future regulatory policy.