In a significant victory for the Obama administration, Chief Justice John G. Roberts Jr. on Thursday refused to block an Environmental Protection Agency regulation limiting emissions of mercury and other toxic pollutants from coal-fired power plants.

The decision comes three weeks after the full Supreme Court, in a highly unusual move, blocked another major Obama administration rule that would limit planet-warming greenhouse gas pollution from coal plants.

Opponents of Mr. Obama’s environmental policies were buoyed by the high court’s decision to halt the global warming rule, known as the Clean Power Plan, reading it as a sign that the court was willing to halt other regulations while they undergo changes and review. But legal experts said the chief justice’s decision on Thursday signaled that they might not be successful in further attempts to halt environmental rules while they are still subject to legal challenges.

“This is a pretty strong way of sending a signal that the fact that the court granted a stay of the Clean Power Plan was highly extraordinary, and they don’t want to be inundated with these,” said Jeffrey Holmstead, a lawyer with the firm Bracewell and a deputy administrator of the E.P.A. in the George W. Bush administration. “I think this is Justice Roberts’s effort to say that the Clean Power Plan is an extraordinary situation.”

The order was issued solely by Chief Justice Roberts, who did not refer the question to the full court.

Chief Justice Roberts rejected an application from 20 states that said a federal appeals court in Washington had effectively thwarted their victory in the Supreme Court in June, when the justices ruled that the E.P.A. had failed to take into account the punishing costs its mercury regulation would impose. In that 5-to-4 decision, Michigan v. Environmental Protection Agency, the Supreme Court ruled that the agency had run afoul of the Clean Air Act by deciding to regulate the emissions without first undertaking a cost-benefit analysis to show the regulation to be “appropriate and necessary.”