“E.P.A.’s stay, in other words, is essentially an order delaying the rule’s effective date, and this court has held that such orders are tantamount to amending or revoking a rule,” Judges David Tatel and Robert Wilkins wrote. The third member of the three-judge panel, Janice Rogers Brown, dissented.
The judges said that the agency had the right to reverse the methane regulations but would have to undertake a new rule-making process to undo the Obama administration’s regulation.
An E.P.A. spokeswoman said the agency was reviewing the opinion and would weigh its options.
Critics say the Trump administration has improperly delayed other regulations as well, and have challenged a May E.P.A. decision to suspend for 90 days a rule aimed at cutting methane emissions from landfills.
In June, the Interior Department also delayed for two years a set of rules that would have limited the release of methane from wells on federal and tribal lands. That rule has been in the administration’s cross hairs, but an attempt to reverse it in Congress failed when Senator John McCain, Republican of Arizona, and two other Republicans defected.
The administration has also used the delay tactic to stop a Food and Drug Administration rule requiring restaurants to list the calories in the food they sell and a Labor Department regulation mandating that financial advisers put consumers’ best interests ahead of their own.
The E.P.A. has been in the vanguard of the administration’s attempts to dismantle what Mr. Trump and his advisers consider an oppressive regulatory state. In a February executive order, Mr. Trump instructed cabinet officers to look for every opportunity “to alleviate unnecessary regulatory burdens placed on the American people.”
Monday’s court ruling signals that this will not be accomplished overnight.
The administration has had some success in delaying or reversing former President Barack Obama’s climate change and environmental policies, but other actions face serious legal hurdles. After the E.P.A. allowed farmers to use a pesticide called chlorpyrifos that has been found to harm children’s brains, California and six other states challenged the decision.
And the effort to reverse the Clean Power Plan regulation on power plant carbon emissions — the rule at the heart of Mr. Obama’s climate change agenda — could take years. Mr. Pruitt is expected to publish the details of his plan to repeal the regulation in the coming weeks.
David Doniger, director of the climate and clean air program at the Natural Resources Defense Council, said he believed the administration would be on the losing end of those battles.
“This is the first of what we hope will be many court setbacks for Scott Pruitt, whose devotion to the law is rhetorical and not real,” he said.
The methane rule was part of a broad suite of climate regulations enacted by Mr. Obama. Methane is a potent greenhouse gas 25 times more powerful than carbon dioxide.
Oil and gas companies have argued that the rule requiring them to report and fix any methane leaks in their equipment is an unnecessary burden because many oil-producing states already have their own regulations. The E.P.A. announced on June 5 that it was suspending enforcement of the rule, arguing that the industry had not had enough opportunity to comment. The court rejected that argument.
“The court’s decision ends the continued pollution by the oil and gas industry that’s been illegally allowed by Pruitt,” said Fred Krupp, president of the Environmental Defense Fund, one of the plaintiffs in the case.
Reid Porter, a spokesman for the American Petroleum Institute, said that standards set in 2012 were already reducing methane emissions. “A stay is needed to allow for regulatory certainty as E.P.A. continues the formal process to review the rule making,” he said in a statement.
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