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The federal agency responsible for protecting North Atlantic right whales misrepresented the views of its own scientists to justify its decision to open long-closed fishing grounds off Nantucket last year, putting the critically endangered species at greater risk, according to an explosive complaint filed last week with a government inspector general.

In addition, lawyers for the National Marine Fisheries Service made false or misleading statements about the agency’s decision, which is being challenged in federal court, according to the Public Employees for Environmental Responsibility, a Washington-based group that represents government whistle-blowers.

“NMFS either misrepresented the advice of its own scientists or failed to follow normal procedures regarding seeking such advice; made false or misleading statements; omitted important information; and failed to use the best available science in its decision,” wrote Timothy Whitehouse, executive director of the group.

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Without citing its sources, the group told the inspector general of the Commerce Department, which oversees the Fisheries Service, that it has “reason to believe” that there are e-mails, memos, and other internal communications that support their allegations that the agency’s officials were responsible for “blatantly mischaracterizing” the recommendations of its scientists on whether to open 3,000 square miles of popular feeding grounds for right whales to fishermen. The move, made under pressure from the fishing industry, outraged environmental advocates.

“An internal review process would likely reveal a disagreement within the agency, or a failure to take into account the advice of . . . its own right whale scientists, or true ‘agency expertise,’ ” Whitehouse wrote.

Officials at the Fisheries Service and the Commerce Department declined to comment on the complaint, which was filed last Monday. An official at the inspector general’s office said he had yet to review the complaint.

Lawyers at the Boston-based Conservation Law Foundation, which sued the agency over its decision, called the accusations “deeply troubling.”

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“These troubling allegations suggest unlawful conduct at the highest levels of the agency and possibly among lawyers at the Department of Justice,” said Erica Fuller, a senior staff attorney at the Conservation Law Foundation. “The officials charged with protecting this species appear willing to misrepresent the facts and the science to both the court and the public because they’re hell-bent on doing nothing that might save right whales from extinction.”

Department of Justice lawyers who are defending the agency against CLF’s lawsuit did not respond to requests for comment. Late Wednesday, they filed a motion in federal district court in Washington, D.C., to seal the complaint from public view.

Right whales are among the most endangered species on the planet. There are believed to be fewer than 400 left, and their population has declined by about 20 percent since 2010. Ten have been found dead so far this year.

In that time, when a cause of death could be determined, 64 percent were found to have died from entanglements in fishing gear, according to the agency. The rest were killed by vessel strikes. None are known to have died of natural causes since 2010.

The decision to open the fishing grounds south and east of Nantucket would allow fishermen to use gillnets — a wall of netting that rises vertically in the water — that scientists say pose a significant threat to right whales, which have been found to inhabit the area in increasing numbers.

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But agency officials have downplayed those concerns and didn’t address them when they issued their decision to open the area.

“Reopening the closed areas would not affect right whales or their critical habitat in a manner beyond what was considered in prior” reviews of the Endangered Species Act, which requires that any fishing not “jeopardize the continued existence” of an endangered species such as right whales, agency lawyers wrote in a federal court filing.

As a result, they argued, the agency wasn’t required to conduct a deeper review and consult with all branches of the Fisheries Service before opening the closed areas.

The Conservation Law Foundation argued that such a review was legally required, because the agency was basing its decision on old assumptions and didn’t consider new findings on the dangers of entanglements in fishing gear.

In his complaint to the inspector general, Whitehouse alleges that agency officials either failed to consult scientists who would have advised them about the potential dangers of reopening the area or ignored many scientific papers those scientists wrote that warned of the dangers of fishing gear to right whales.

The agency’s lawyers “falsely claimed” in court that they had examined scientific papers that were published after the agency completed an environmental impact statement about reopening the area, the complaint alleged.

He said he had reason to believe that agency officials ignored advice on the closures from their scientists.

“PEER believes the decision could have been made at the upper levels of NMFS to hide the critical facts that the closed areas in question provide refuge to right whales, and eliminating them will harm this endangered species,” Whitehouse wrote.

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Representatives of the scallop industry, which has been allowed to access the newly opened areas and has earned millions of dollars from their catch, said they were operating safely.

“Scallopers have been fishing for years, and there’s not a single known interaction with a right whale,” said Drew Minkiewicz, an attorney at the Fisheries Survival Fund in Washington, D.C., which represents the scallop industry. “If we’re not impacting them, then why should we be restricted from the area?”

But scientists say that other fisheries, such as those that use fixed gear like lobster traps, pose a grave threat to right whales. That threat has increased in the waters off Nantucket, where more right whales have been spotted in recent years.

“What we know, and what our peer-reviewed science has shown for the last many years, is that the probability of entanglement is greater than zero in an area where there is fishing activity,” said Julie van der Hoop, a marine biologist at the Woods Hole Oceanographic Institute who studies right whales. “Entanglements, when they occur, can lead to injury and death.”

Scott Kraus, chief scientist of marine mammals at the New England Aquarium, said he thought the complaint had merit.

“The NMFS behavior is unsurprising to those of us who have worked with the agency for decades,” he said. “It is a perfect example of the conflict between the agency’s two responsibilities: promote and manage the nation’s fisheries, and protect species. As in most prior cases, this looks like the fishermen win.”

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David Abel can be reached at dabel@globe.com. Follow him on Twitter @davabel.