Under the change announced Friday, companies would have to commit to take additional measures if they kill or injure more eagles than they have estimated they would, or if new information suggests that eagle populations are being affected. The permits would be reviewed every five years, and companies would have to submit reports of how many eagles they kill. Now such reporting is voluntarily, and the Interior Department refuses to release the information.
"This is not a program to kill eagles," said John Anderson, the director of siting policy at the American Wind Energy Association. "This permit program is about conservation."
Wind farms are clusters of turbines as tall as 30-story buildings, with spinning rotors as wide as a passenger jet's wingspan. Though the blades appear to move slowly, they can reach speeds of up to 170 mph at the tips, creating tornado-like vortexes.
Flying eagles behave like drivers texting on their cellphones; they don't look up. As they scan below for food, they don't notice the industrial turbine blades until it is too late.
No wind energy company has obtained permission authorizing the killing, injuring or harassment of eagles, although five-year permits have been available since 2009. That puts the companies at legal risk and discourages private investment in renewable energy.
It also doesn't necessarily help eagles, since without a permit, companies are not required to take steps to reduce their impact on the birds or report when they kill them.
The new rule makes clear that revoking a permit - which could undermine investments and interest in wind power - is a last resort under the administration's energy policy.
"We anticipate that implementing additional mitigation measures ... will reduce the likelihood of amendments to, or revocation of, the permit," the rule said.
Conservation groups, which have been aligned with the wind industry on other issues, said the decision by the Interior Department sanctioned the killing of an American icon.
"Instead of balancing the need for conservation and renewable energy, Interior wrote the wind industry a blank check," said Audubon President and CEO David Yarnold in a statement. The group said it will challenge the decision.
The wind energy industry has said the change mirrors permits already in place for endangered species, which are more at risk than bald and golden eagles. Bald eagles were removed from the endangered species list in 2007 but are still protected under two federal laws.
The regulation published Friday was not subjected to a full environmental review because the administration classified it as an administrative change.
"The federal government didn't study the impacts of this rule change even though the (law) requires it," said Kelly Fuller, who formerly headed up the wind campaign at the American Bird Conservancy. "Instead, the feds have decided to break the law and use eagles as lab rats."
The Fish and Wildlife Service said the new rule enables it to better monitor the long-term environmental effects of renewable energy projects.
"Our goal is to ensure that the wind industry sites and operates projects in ways that best minimize and avoid impacts to eagles and other wildlife," the agency said in a statement.
Last month, Duke Energy Corp. pleaded guilty to killing eagles and other birds at two wind farms in Wyoming, the first time a wind energy company has been prosecuted under a law protecting migratory birds.
A study by federal biologists in September found that wind farms since 2008 had killed at least 67 bald and golden eagles, a number that the researchers said was likely underestimated.
It's unclear what toll, if any, wind energy companies are having on eagle populations locally or regionally. Gunshots, electrocutions and poisonings almost certainly kill more bald and golden eagles than wind farms. But with the industry still growing, the toll could grow, too.
A recent assessment of status of the golden eagle in the western U.S. showed that populations have been decreasing in some areas and rising in others.