The ruling earlier this month by the Environmental Protection Agency earlier opens the way for regulation of six heat-trapping gases without new laws passed by Congress.
Livestock farms emit carbon dioxide from the tailpipes of machinery and trucks, while waste from cattle also emits methane, a powerful greenhouse gas.
The National Cattlemen's Beef Association filed a petition in the D.C. Circuit Court of Appeals this week, saying EPA climate regulations would hurt large farms.
"This unilateral move by the EPA jeopardizes our ability to remain competitive in the global marketplace," said Tamara Theis, chief environmental counsel for the National Cattlemen's Beef Association.
She said potential EPA rules could force many farms to get permits to emit greenhouse gases or slow operations. If farms had to buy the permits in a market or curtail beef output it could help force many of them to close.
The Obama administration has always said it favors climate legislation in Congress over action by the EPA. But the agency made the move as the climate bill faces an uncertain future in the Senate amid opposition from lawmakers in states that produce and burn large amounts of fossil fuels.
By spurring the EPA to act, the administration indicated greenhouse gases will be regulated one way or another. The move was designed to spur businesses to lobby Congress to act on climate legislation, as companies have a bigger say in that process.
But analysts have said that nearly any action the EPA takes on climate before a new bill gets passed would be vulnerable to litigation and Congressional action.