By sacrificing a few bald eagles, the Obama administration may have opened a can of worms.

In a bid to give alternative energy sources a boost, the U.S. Fish and Wildlife Service has quietly granted a California wind energy farm a permit to kill a limited number of endangered bald and golden eagles that get sliced up in its giant turbines. But last week’s free pass is sparking anger from wildlife advocates and from free market advocates who ask why they don’t qualify for the same dispensation.

The American Bird Conservancy filed a lawsuit last week against the 6-month-old federal rule expanding permits for killing bald and golden eagles from a maximum of five to 30 years, charging the Interior Department with “multiple violations of federal law.”

Conservancy spokesman Bob Johns said the organization is on board with green energy but the Obama administration has gone too far with incentives for the wind industry. The incentives include optional guidelines on environmental rules and production tax credits.

“We know we need renewables, and that’s fine. We’re not saying shut them down, we’re just saying, ‘Hey, enough’s enough, bring them into the same ballpark that everyone else is in,’” said Mr. Johns. “Give them regulations, tell them where they need to site these things, where they shouldn’t site them. Don’t give them a set of, ‘Gee, it would be nice if you did this, but if you don’t, it’s OK.’”

Last week, the Fish and Wildlife Service ruffled feathers by issuing what officials called a first-of-its-kind permit that allows a 50-turbine Northern California wind farm to kill up to five golden eagles over five years. In exchange, the developer agreed to retrofit 133 utility poles to reduce eagle deaths by electrocution.

“We can’t solve the problem of eagle mortality at wind farms overnight,” Fish and Wildlife Service Director Daniel Ashe said in a statement. “But this common-sense solution merits the support of all who advocate for the long-term conservation of eagles.”

“This is not a program to kill eagles,” John Anderson, director of siting policy at the American Wind Energy Association, told The Associated Press late last year. “This permit program is about conservation.”

Among those stunned by the agency’s move were residents of King Cove, Alaska. Interior Secretary Sally Jewell ruled in December that those in the remote fishing village could not build an 11-mile gravel road to a nearby airport because it would affect eelgrass that serves as a way-stop meal for migratory birds.

“We’d have much less impact on the birds with our road than these wind farms have on the eagles,” said Della Trumble, a spokeswoman for the King Cove Corp. and the Agdaagux tribe. “It’s another slap in the face. It doesn’t make sense.”

The administration’s preferential treatment is designed to help boost the wind energy industry as part of a strategy to reduce fossil fuel use, which President Obama has described as a necessary step in combating climate change.

“The changes in this permitting program will help the renewable energy industry and others develop projects that can operate in the longer term while ensuring bald and golden eagles continue to thrive for future generations,” Ms. Jewell said in a December statement.

But free market advocates argue that the Obama administration is playing favorites by letting the wind industry bypass regulations that hold back other energy providers. The Bureau of Land Management decided last week to cordon off 400,000 acres from energy development in Utah and Colorado in anticipation of a listing to preserve the numbers of the Gunnison sage-grouse.

Michael Sandoval, an energy analyst with the Independence Institute in Denver, said there is inevitably enormous outrage when sea gulls or ducks are coated with oil after a spill, but much less concern over wind turbines that chop eagles in half or cause bats to explode.

“Preferred energy policy favoring wind produces double standards. Think of the rancor if oil and gas companies were allowed such a government dispensation,” said Mr. Sandoval. “Thirty years represents not only the theoretical life cycle of the turbines themselves, but an eternity in public policy. No other industry is allowed ‘takings’ permits that last an entire generation.”

The Interior Department’s decision to extend by sixfold the permit period prompted Mr. Sandoval to create a video game, “Greed Energy Kills,” which depicts cartoon birds and bats trying to avoid turbines.

Wind farms typically feature clusters of turbines that can rise as high as a 30-story building, with whirling rotors that can reach more than 150 mph at the tips of the blades. Eagles scanning the ground below for a meal often do not see the danger until it is too late.

The conservancy lawsuit cites the 1940 Bald and Golden Eagle Protection Act, which provides fines and jail time for those who kill eagles on purpose or by accident. The law even prohibits possession of eagle feathers, talons and beaks.

In 2009, the Fish and Wildlife Service added a provision to the 1940 law allowing permits for eagle kills when they are incidental to an otherwise legal activity, such as construction or transportation projects.

Since the 1980s, wind turbines have killed an estimated 2,000 to 3,000 eagles, but the industry has paid only one fine, Mr. Johns said.

“If you or I get caught with an eagle feather, we’ve got some serious explaining to do. We’re going to pay a hefty fine,” said Mr. Johns. “There’s no exception noted in the law for the wind industry. The notion that somehow they’re entitled when the law doesn’t provide for it is ridiculous.”

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