This photograph of a two-headed trout comes from a report commissioned by Idaho-based J.R. Simplot in an attempt by the phosphate mining company to justify more selenium pollution in eastern Idaho watersheds. Last week, Simplot officials denied any knowledge of the photograph.

Less than a week after J.R. Simplot Company officials denied knowledge of two-headed trout pictures taken near their Smoky Canyon Mine in eastern Idaho, a report confirmed the deformities.

A 694-page draft report, prepared for Simplot by Formation Environmental, of Boulder, Colo., and HabiTech,  of Laramie, contains pictures of the trout. The August 2010 report is titled “Interpretive Findings for Field and Laboratory Studies and Literature Review in Support of a Site-Specific Selenium Criterion, Smoky Canyon Mine.”

The Smoky Canyon Mine is located in Idaho on the Caribou-Targhee National Forest about 10 miles west of Afton. Creeks polluted by the mine drain into the Salt River,  which drains into Palisades Reservoir on the Snake River.

Last week, Simplot spokesman David Cuoio said his company didn’t know about pictures of two-headed fish resulting from pollution from the phosphate mine

“We’re not aware of any two-headed fish near our facilities,” he said. “I’m not sure who took those pictures or where they were taken.”

Despite the report bearing his company’s name, Cuoio did not retract the statement Monday. He said the company was using an “open, transparent and scientifically based approach to protect the environment.”

Simplot officials are using the report in an attempt to justify an increased level of selenium pollution near the mine. On Jan. 30, Simplot submitted a proposal to the state of Idaho to ease water-quality standards in Sage and Crow creeks, where the deformed fish were found.

“We have been working with the state of Idaho and other state and federal agencies, including EPA, to conduct studies that may lead to science-based, site-specific water-quality standards regarding selenium for the locations around Sage Creek and Crow Creek adjacent to our Smoky Canyon Mine, as provided by the Clean Water Act,” Cuoio said in a statement Monday. “Our proposal for such a standard, along with all relevant supporting technical information, was submitted to the state of Idaho on Jan. 30, 2012.”

The request comes despite a scathing U.S. Fish and Wildlife Service critique that found some portions of the Simplot research “highly questionable” and riddled with “confounded data.”

The critique, authored by U.S. Fish and Wildlife Service biologist Joseph Skorupa, found that the Simplot report underestimated how many fish would suffer deformities in waters adjacent to the Smoky Canyon Mine. Three independent peer reviewers subsequently agreed with more than 94 percent of Skorupa’s conclusions, according to the critique.

In the Simplot report, researchers attempted to prove that a selenium level of 22 parts per million in the eggs of trout in Sage Creek and Crow Creek would result in a marginal impact on the fish population.

“In the expert opinion of our biologist, the proposed site-specific selenium concentrations would result in serious harm to fish and wildlife, if implemented,” U.S. Fish and Wildlife Service spokesman Chris Tollefson said Tuesday. “Our review found significant flaws in the scientific justifications presented in the Smoky Canyon Mine document and concluded that those justifications were inadequate to support the site-specific selenium water-quality criterion being proposed.”

Skorupa was asked to review the document in a strictly advisory capacity, and the U.S. Fish and Wildlife Service will not play a role in the decision on whether to relax selenium pollution standards around the mine Tollefson said.

Skorupa’s critique found that Sage Creek exceeded even Simplot’s proposed standard of 22 parts per million most of the time. Of seven samples taken from the creek, five exceeded 22 parts per million, ranging from 26.8 to 40.3 parts per million. Of those, the number of fish expected to survive for 15 days after hatching was zero.

Aside from two-headed fish, the Simplot report contains photographs of numerous fish deformities from the creeks around the mine, including those of the eye, jaw, fin and spine. In one case, a photo shows a spinal deformity so severe the fish was bent back on itself.

Skorupa also calls foul on reported fish populations in the contaminated creeks. Researchers did not account for fish that might migrate into the polluted creeks to occupy the habitat left empty by fish that failed to reproduce, he found.

“Low-quality polluted habitats that poison fish and birds can, nonetheless, be highly attractive,” Skorupa wrote.

Fish, like other species, will try to occupy all available habitat, said Marv Hoyt, Idaho director of the Greater Yellowstone Coalition.

“As these fish fail to reproduce at the level that they should be, so fish in-migrate from Crow Creek at the Salt River,” Hoyt said. “It’s a population sink.”

The element selenium is a by-product of phosphate mining. The element is an essential human nutrient in small doses but is a known toxin at higher doses.

Selenium has been blamed for a number of livestock die-offs near phosphate mines in southeast Idaho, including 600 sheep and 18 head of cattle, Hoyt said.

The Smoky Canyon Mine is a Superfund site, and Simplot hoped the report would help the company avoid paying the “tens of millions of dollars to clean it up,” Hoyt said.