Lawmakers describe the provision in the spending bill as a necessary intervention in a wildlife dilemma that some say has spun out of control. Sixty-six wolves were reintroduced to the Northern Rockies from Canada in the mid-1990s; there are now at least 1,650.
But legal experts warn the administration's support of lifting protections for the animals opens the door to future meddling by lawmakers catering to anti-wildlife interests.
The endangered act has long been reviled by conservatives who see it as a hindrance to economic development. Now, the administration's support for the wolf provision signals that protections for even the most imperiled animals, fish and plants are negotiable given enough political pressure, experts said.
Officials in Montana and Idaho already are planning public hunts for the predators this fall, hoping to curb increasingly frequent wolf attacks on livestock and big game herds.
"The president could have used some political capital to influence this and he didn't," said Patrick Parenteau, a professor of environmental law from the Vermont Law School. "The message to the environmental community is, don't count on the administration to be there" for the protection of endangered species.
Environmentalists still count Obama as an ally on other issues, ranging from climate change and wilderness preservation to oil and gas exploration. Yet experts in wildlife law say that in the scramble to pass the budget, the administration is circumventing one of the country's bedrock environmental laws.
That's a bitter pill for conservationists, who hoped a Democratic White House would more aggressively protect a law many say was ignored under the Bush administration.
The next potential blow to the law already is looming. A 2012 budget request from the Department of Interior would impose a sharp spending cap on a program that allows citizens to petition for species to be listed as endangered.
Those petitions were used for the majority of the species added to the list over the last four decades.
"We are having the worst attack on the Endangered Species Act in 30 years while we have a Democratic Senate and a Democratic White House," said Kieran Suckling with the Center for Biological Diversity. "They are trying to shut citizens and scientists out of the endangered species process."
To date, the Obama administration has listed 59 species as endangered - a rate of about 30 a year, according to Suckling's group, which closely tracks endangered species issues.
That's up significantly from the Bush years, when the average was eight per year, but far behind the 65 species per year under the Clinton administration.
Western lawmakers who backed the budget bill rider said the wolf issue was unique and merited special intervention. Federal judges over the last decade had repeatedly blocked attempts to downgrade the legal status of an animal population most biologists agreed was thriving.
Meanwhile, wolf attacks have generated resentment among ranchers and sportsmen. Those groups are increasingly frustrated they have been unable to strike back against the predators.
J.B. Ruhl, an expert in the Endangered Species Act at Florida State University, warned against reading too much into the wolf provision, which was latched onto a must-pass bill needed to avert a government shutdown.
"It seems to me the planets had to be aligned just right to make this happen," Ruhl said. "There might be a wing of the Republican party that would love to see the Endangered Species Act reformed, but I don't think they are going to be able to ram that through anytime soon."
Support within the Obama administration for lifting wolf protections predates the budget negotiations. That stance mirrors the government's actions under the Bush administration, when officials first proposed lifting protections.
The White House referred questions to the office of Interior Sec. Ken Salazar.
Interior spokeswoman Kendra Barkoff refused to directly address the legislation. She said the agency views the Endangered Species Act as a "critical safety net" that has prevented the extinction of hundreds of imperiled species.
"It is our responsibility to continue implementing the law," she said.
Some critics of congressional intervention characterized the budget bill rider as Republican meddling on an issue best settled through open hearings. Rep. Edward Markey of Massachusetts, the top Democrat on the House Natural Resources Committee, accused the GOP of wanting to "kill wolves instead of cutting pork."
Democratic Sens. Ben Cardin of Maryland and Barbara Boxer of California also have spoken against the measure.
Yet it had a degree of bipartisan support heading into the budget negotiations. Montana's two Democratic senators, Jon Tester and Max Baucus, both took credit for getting the language into the budget bill.
"It was a little hard persuading Sen. Boxer and Sen. Cardin that we're not gutting the Endangered Species Act," Baucus said in an interview. "They don't have the same understanding of the wolf problem that we have."
Congress has stepped into divisive wildlife issues before, such as in the 1980s when it exempted from the endangered act a hydroelectric dam proposed by the Tennessee Valley Authority. The dam was constructed in an area inhabited by an endangered fish, the snail darter.
During the West Coast timber wars of the 1990s, Congress used a legislative rider to allow logging despite potential threats to the endangered spotted owl.
The case of wolves is different because lawmakers are directly targeting an endangered animal, not merely promoting economic development a species was thought to be impeding.
The Supreme Court made clear with a ruling in the snail darter case that legislative riders do not violate the U.S. Constitution, said Fred Cheever with the University of Denver's Sturm School of Law.
Still, Cheever said the intervention with wolves still represents a dangerous precedent because it is being used to negate rulings made by federal courts. That effectively eliminates the judicial branch's role in deciding what legal protections are needed to prevent a species from going extinct.
"It's a scary road to go down," Cheever said. "Everything is a bargaining chip, from bombers to baby care. Riders aren't limited to the Endangered Species Act."