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updated 7/29/2011 3:29:13 PM ET 2011-07-29T19:29:13

Facing an internal investigation that included questions about a polar bear deaths study that Al Gore cited in "An Inconvenient Truth", a federal scientist went on the offensive Thursday, filing a complaint alleging persecution from within the Interior Department.

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Charles Monnett, a wildlife biologist with Interior's ocean energy agency, had earlier been questioned by investigators and was then placed on administrative leave.

The complaint alleges that Interior Department "officials have actively persecuted Dr. Monnett, acted on hearsay and rumors, gratuitously tarnished his reputation and substantially disrupted important scientific research."

Agency spokeswoman Melissa Schwartz told msnbc.com that "the agency placed Mr. Monnett on administrative leave for reasons having nothing to do with scientific integrity, his 2006 journal article, or issues related to permitting, as has been alleged. Any suggestions or speculation to the contrary are wrong."

While she could not comment on the specifics of the investigation, she added that "all of the scientific contracts previously managed by Mr. Monnett are being managed by the highly qualified scientists."

The complaint specifically alleges that ocean agency Director Michael Bromwich and investigator Eric May committed scientific and scholarly misconduct.

Investigators questioned Monnett last February, according to the complaint, which included a partial transcript of questions and answers that centered around how he and another scientist reached the conclusion that several observed polar bear deaths were tied to shrinking sea ice in the Arctic.

Story: Arctic also sees heat wave, on course for record ice melt

Monnett is being supported in his complaint by the activist group Public Employees for Environmental Responsibility, which suggested that the agency was being pressured by oil companies seeking to drill farther out at sea in the Arctic.

"Ever since this paper was published, Dr. Monnett has been subjected to escalating official harassment," PEER Executive Director Jeff Ruch said in a statement. "This is a cautionary tale with a deeply chilling message for any federal scientist who dares to publish groundbreaking research on conditions in the Arctic."

Ruch noted that while Interior earlier this year adopted its first policy to protect scientists from political interference, "this case illustrates that federal scientists working in controversial areas today are at greater risk than during the Bush administration."

Similar studies showing a connection between shrinking sea ice and polar bear deaths have since been peer reviewed and published.

Earlier this month, scientists reported polar bear cubs that had to swim longer distances than other cubs appear to have a higher mortality rate.

Story: Fewer polar bear births tied to less sea ice

The Bush administration listed polar bears as threatened under the Endangered Species Act because of the decrease in their Arctic ice habitat. That decision survived a legal challenge last month, and this month, Canada listed polar bears as a species at risk.

Reuters contributed to this report.

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