But in a rebuke that conservationists called embarrassing to Fish and Wildlife, and that questions its will to move forward with a reintroduction that North Carolina land owners oppose, the four scientists who conducted the research on which the agency relied fired off a letter Tuesday saying the justification for the new plan was full of “alarming misinterpretations.”

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The genetic purity of red wolves in captivity is not at risk, said Lisa Faust, the author of the research and vice president of conservation and science at Chicago’s Lincoln Park Zoo. Furthermore, contrary to Fish and Wildlife’s assessment, there is no danger of red wolves going extinct under the current management plan.

Faust and environmentalists said the federal government’s argument that wolves in captivity are in danger of extinction was a slap in the face of the agency’s partners who maintain breeding populations at zoos nationwide. At least two of the researchers who conducted the red wolf population viability analysis, or PVA, are intimately involved in the captive breeding program.

“It was frustrating to me that they used the science this way,” Faust said. “We knew we needed to respond right away. I think that certainly the people in [captive breeding] were proud of that program, which is extremely well managed. We hold it up as a flagship restoration program.”

Fish and Wildlife partnered with scientists and conservation groups from the outset of its vow to fulfill a wish by Congress 30 years ago to restore red wolves to at least a portion of their historic habitat in the southeast. A few wild wolves were bred with captive wolves at zoos, and a small population was set free at the Alligator River National Wildlife Refuge.

The program was considered a success until the population started to decline around 2010. Conflicts arose with land owners who considered wolves a threat. Although the wolves were protected, the state allowed hunters to shoot coyotes, leading to wolves being shot dead by hunters who claimed they made a mistake. Funding for the program was cut, and some of its managers, feeling under siege, quit or accepted reassignments.

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Two weeks after Fish and Wildlife announced its new management plan, a federal-district court in North Carolina sided with a coalition of environmental groups that fought the agency’s decision to permit land owners to kill wolves they considered a nuisance. The court ruled that for that to happen, the landowners and agency must prove the wolf is a direct threat to humans and livestock.

For many conservationists, the funding cuts, staff reductions, kill permits and the use of science it paid for and was misinterpreted are proof that Fish and Wildlife is backing away from restoring red wolves.

Jeff Fleming, a spokesman for Fish and Wildlife’s southeast region, characterized the discrepancy as different interpretations of the science Faust and her team submitted. “We appreciate the feedback,” he said. Fish and Wildlife says it believes that the genetic purity of the wolves needs to be higher than the marker determined by the research.

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“We’re going to move forward,” Fleming said, and “this will be taken into account as we move forward” with a process that could take more than a year to complete and implement. “I don’t know if it’s a disagreement.”

That’s exactly what it is, said Ben Prater, southeast program director for Defenders of Wildlife, a nonprofit group that until March was one of Fish and Wildlife’s partners in the red wolf recovery program. When Cindy Dohner, Fish and Wildlife’s southeast regional director, announced the proposal for a new red wolf management plan and cited the science he had read, Prater was taken aback.

“The science — many of us looked at it — was fairly clear. We were astonished that they saw that the captive population was in dire straits,” Prater said. “I think to have claimed that the captive population was somehow in trouble flies in the face of the work done by the species survival program over the last 30 years. This was an award-winning program. Their mandates are based on science, and it’s very disappointing to see this misinterpretation.”

Ron Sutherland of the Wildlands Network, another nonprofit conservation group that observes red wolves, wondered whether Fish and Wildlife’s decision was based more on politics than science.

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“I think the most likely scenario is they wanted to go on the retreat for political reasons and budget reasons, and they needed some gauze of credibility, so they said the captive population was at risk of extinction,” Sutherland said. “But the report said exactly the opposite.”

Fleming flatly disagreed. “If everything they’re saying was true, we wouldn’t be doing any of what we’re doing,” he said. “We discovered years ago that we were doing things that were inconsistent with the rule” that governs the protection of endangered species.

Namely, Fleming said, some of the promises made to landowners that wolves would be more carefully managed were broken, and they had reason to complain. “We need landowners, conservationists and everyone to know we’re going to do what we say we’re going to do.”

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He expressed frustration with conservationists: “This kind of stuff is not constructive.”

But, Prater and Sutherland said, Fleming’s perspective, that the conclusion of the research team was left to interpretation, is not credible. “If anybody knows their science, it’s the team that researched it,” Sutherland said. “And if they’re saying Fish and Wildlife got it 100 percent backward, that’s just what they’re saying.”