An E.P.A. spokeswoman, Melissa Harrison, said the agency intended to move forward with the rule.

Ms. Harrison said that since the court’s ruling was about how and when the agency considered costs in its decision about limiting mercury and other toxic emissions and not the agency’s authority to limit them over all, the E.P.A. was committed to protecting the public “from the significant amount of toxic emissions from coal- and oil-fired electric utilities and continue reducing the toxic pollution from these facilities.”

The mercury regulation was one in a series of new Clean Air Act regulations from the Obama administration that President Obama hopes to build into a major environmental legacy. Later this summer the agency is expected to release a set of landmark climate change rules limiting greenhouse gas pollution from power plants — restrictions that have faced legal challenges from industry.

In the term that ended in June 2014, the justices heard cases on two other sets of Clean Air Act regulations — one aimed at limiting power plant pollution that wafts across state lines, the other at cutting planet-warming greenhouse gas emissions. The E.P.A. won the first case and largely prevailed in the second, though the Supreme Court indicated that it remained prepared to impose limits on the agency’s regulatory authority.

Congressional Republicans, who have sought to limit the Clean Air Act rules, celebrated Monday’s decision.

“From its ozone to greenhouse gas to navigable waters rules, the E.P.A. continues to burden the public with more and more costs even as so many are still struggling to get by and improve their lives in this economy,” said Kevin McCarthy of California, the House majority leader. “The Supreme Court’s decision today vindicates the House’s legislative actions to rein in bureaucratic overreach and institute some common sense in rule making.”

Among the remaining questions is whether the current rule will stay in place as the E.P.A. completes its revision of the language, and how long that revision will take.