A number of other Trump administration actions to undo regulations it inherited, including a rule on grizzly bear protection and another on chemical spills, are likely to receive close scrutiny from the courts.

Mr. Pruitt had imposed a 90-day moratorium, which he later extended to two years, on enforcement of parts of the E.P.A. methane regulation. He had also argued that his action was not subject to court review. But the appeals court ruled that the agency’s decision was “unreasonable,” “arbitrary” and “capricious.” The agency, it said, did not have authority under the Clean Air Act to block the rule.

“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.