Mr. Johnson said he was “extremely disappointed” in the court decision “because it’s overturning one of the most significant and health-protective rules in our nation’s history.”  But on climate change, he said laws like the Clean Air Act were “ill-suited” to the complexities of regulating greenhouse gases.  Mr. Johnson’s comments appeared as a preface to a report by the E.P.A. staff sketching out how the emission of heat-trapping gases, particularly by vehicles, might be handled under the Clean Air Act. The report was intended to address a Supreme Court directive that the agency decide whether such gases threaten people’s health or welfare. But it also reflects the deep disapproval of controls on such gases by the White House and agencies like the Transportation, Agriculture and Commerce Departments.  In effect, Mr. Johnson was simultaneously publishing the policy analysis of his scientific and legal experts and repudiating its conclusions.  The Clean Air Interstate Rule, which covered states in the eastern half of the country, set new requirements for controls on major pollutants emitted by industry, particularly the electric utilities. At its most stringent, it would have required, beginning in 2015, 70 percent reductions in sulfur dioxide and 60 percent reductions in nitrogen oxide from 2003 levels.  At the time the interstate pollution rule was adopted, the E.P.A. estimated that, when fully in effect after 2015, it would cut by 13,000 annually the number of premature deaths from breathing polluted air.  The court ruling, combined with a court decision this year striking down an E.P.A. rule controlling mercury emissions from power plants, means that virtually all controls on the electric utility industry by the Bush administration have no force.  “The implications are huge,” said Lisa Heinzerling, a professor at Georgetown University Law Center. “This is the administration’s major air pollution initiative.”  The restrictions were designed, Ms. Heinzerling said, to deal comprehensively with a variety of air pollution issues, including the interstate transport of pollutants and the states’ obligations to enforce standards to protect the public health.  But with the court’s decision, she said, all of the administration’s efforts, aside from those involving vehicles, “are gone.”  “Anything they’ve done that has any relation to pollution control has been invalidated,” she said.  The court decision disappointed even the victors.  Jim Owen of the Edison Electric Institute said, “In our industry, one of the things we crave is certainty, and this goes in the other direction.”  Brent W. Dorsey, the director of corporate environmental programs at Entergy, the large energy producer, added, “With this thing thrown out, we’ve basically thrown the baby out with the bathwater.”  Entergy, one of the companies that brought the case to court, emphasized on Friday that it did not want the whole rule thrown out and that it had challenged only the part that allocated permits for emissions of pollutants around the industry. The company said an 11th-hour change by the E.P.A. had put too much of the cleanup burden on areas using oil and gas for power generation, as Entergy does, and not enough on utilities that burn coal.  Thomas Williams, a spokesman for Duke Energy, which had sued the E.P.A., contesting how the rule allocated the pollution allowances among industries, said in an e-mail message, “It was not the intent of Duke Energy’s participation in this litigation to overturn E.P.A.’s Clean Air Interstate Rule.”  Mr. Williams pointed out that North Carolina, where Duke has several power plants, enacted a law in 2002 that set limits on sulfur dioxide and nitrogen oxide that were even tougher than those in the now-defunct federal rule.  Bill Becker, executive director of the National Association of Clean Air Agencies, said on Friday that few states, aside from North Carolina, had laws that would fill the void created by the court ruling.  “Right now we find ourselves in the twilight zone,” Mr. Dorsey, of Entergy, said. “How do you proceed now? Do we continue to buy emissions allowances? Do we work on putting scrubbers on, or what?”  Entergy backs a legislative remedy proposed by Senator Thomas R. Carper, Democrat of Delaware, that would set long-term limits on pollutants.  While industry and environmental lobbyists both expressed concerns about the impact of the court ruling, they divided along more customary lines on Friday’s second decision, the declaration by Mr. Johnson of the E.P.A. that existing federal laws were “ill-suited” to the regulation of heat-trapping gases.  The Association of International Automobile Manufacturers released a statement saying, in part, “We share concerns that the Clean Air Act, which underwent its last major amendment 18 years ago, does not include all of the tools and criteria needed to address the global issue of climate change, including requirements to balance the economic effects and impacts on U.S. manufacturing jobs along with the environmental considerations.”  Mr. Johnson alluded to the difficulty of applying the Clean Air Act, designed for conventional pollutants like sulfur dioxide and nitrogen oxide, to greenhouse gases.  Because interagency consensus could not be reached on a road map for such regulation, Mr. Johnson said, he was simultaneously publishing his staff’s work and the comments of its critics, which had a definite tinge of hostility toward the E.P.A. regulators.  For instance, the chairman of the Council on Environmental Quality, James Connaughton, wrote that the E.P.A.’s staff “myopically focuses on the Clean Air Act and ignores or understates major intended and unintended consequences that would flow from misapplying decades-old regulatory tools.”  The final E.P.A. document, known as an advance notice of proposed rule making, did not contain a staff analysis about the economic benefits of regulation that had been in an earlier draft. That May 30 draft, which circulated widely in Washington, set the benefits of regulation at up to $2 trillion. The final version, based on the revised assumption that gasoline would cost about $2.20 per gallon in the foreseeable future, estimated the economic benefit at no more than about $830 billion.  Matthew L. Wald contributed reporting.  A version of this article appears in print on , on Page A1 of the New York edition with the headline: 2 Decisions Shut Door on Bush Clean-Air Steps. Order Reprints| Today's Paper|Subscribe
A court ruling and an E.P.A. decision deferred to the next president any significant new effort to fight air pollution.