The US listed polar bears as an endangered species last year
The US government has opted to retain a Bush-era rule that limits protection for polar bears from the effects of global warming.
Environmental groups had been calling for the rule to be lifted, and the US Congress had given Interior Secretary Ken Salazar the power to do so.
Mr Salazar said lifting the rule would create "uncertainty and confusion".
The rule means the government will act only against threats to polar bears that arise in their Arctic habitat.
The US Environmental Protection Agency designated polar bears an endangered species last year, because their habitats were disappearing as ice-caps melted.
Environmentalists seized on the ruling, arguing that endangered species were entitled to heightened protection under US law and that the government was therefore obliged to crack down on the carbon emissions causing global warming.
The Endangered Species Act bars federal agencies from "taking actions that are likely to jeopardise the species or adversely modify its critical habitat", and lays down civil and criminal penalties for people that kill or injure designated animals.
But the Bush administration passed a rule exempting "activities outside the bear's range, such as emission of greenhouse gases" from prohibition.
It is this rule that the Obama administration has decided to let stand.
"The Endangered Species Act is not the proper mechanism for controlling our nation's carbon emissions," Mr Salazar said.
"Instead, we need a comprehensive energy and climate strategy that curbs climate change and its impacts."
But the decision has angered environmental groups.
Mr Salazar's move "only serves to cement the Bush administration's legacy of ignoring global warming science, thus putting the polar bear at further risk of extinction", said Melanie Duchin, a Greenpeace campaigner in Alaska, in a statement.
"Regrettably, it seems to reflect an emerging willingness by the Obama administration to ignore clear scientific imperatives on global warming in the face of industry pressure."