Eagle mortality is more difficult to pin down, though it is clear that eagles are only a small fraction of all birds killed by turbines. A study in the Journal of Raptor Research also published last year reported 85 eagle deaths at wind farms in 10 states over a period from 1997 to 2012.
"If you want to know how many eagles are killed because of wind energy, you can't find that number. That number doesn't exist," Yarnold said. "That's a big part of the problem we have with this rule. It's like they [FWS] haven't done the homework."
Green groups have also voiced skepticism about whether FWS has put in place adequate conservation safeguards.
By applying for a permit, turbine operators agree to a certain amount of oversight from FWS, including a five-year review to determine whether operators are taking steps to minimize bird and eagle mortality on their property.
These steps include switching the turbines on only during times of the day or year when eagles are least likely to be flying overhead, as well as the use of radar or other sighting techniques to spot eagles and shut down turbines when they approach.
Participation in the federal permit program is voluntary. If wind developers do not apply for a permit, however, they risk prosecution for bird deaths at wind farms found to violate any number of federal conservation laws, including the Endangered Species Act, the Migratory Bird Treaty Act, and the Bald and Golden Eagle Protection Act.
Prosecution is rare but may be on the rise. In November, the Department of Justice reached a $1 million settlement with Duke Energy for birds killed at two of the company's wind farms in Wyoming. The settlement marked the first time the federal government had pursued legal action against a wind developer for bird deaths caused by turbines.
Now that the precedent has been set, the threat of litigation will likely to carry more weight. The American Bird Conservancy recently announced that it is considering bringing a lawsuit against the Ohio National Guard for the planned construction of a wind turbine near Lake Erie.
Such proposed litigation and the Duke Energy settlement have also elevated the issue of bird deaths from turbines to a higher profile in the national debate over how to strike a balance between conservation and clean energy.
Contrary to what some environmentalists say, FWS insists that the permitting process actually works to protect wildlife.
"We're not going to issue a permit unless we think there's an overall conservation value," said David Cottingham, senior adviser to the director of the service.
But environmentalists remain unconvinced — a stance that has put them at odds with the wind industry, which defends the permitting process as necessary to provide regulatory certainty for wind developers.
"Most environmental organizations support the wind industry, but what we're saying right now is just because you're producing clean energy, that doesn't mean you have carte blanche to run roughshod over environmental law," said Robert Johns, a spokesman for the American Bird Conservancy.