She also said the agency had to do a better job of explaining its mission to hostile constituencies, including Congress and the agriculture, mining and utility industries.

“We need this agency to reinvent itself, to the extent an agency of 17,000 people can,” Ms. McCarthy said in a staff meeting in a waterfront conference room known as the Fish Shack. “I spend a lot of time protecting what we are doing rather than thinking about what we should be doing. The challenges of today are very different from the challenges of 40 years ago. Not every environmental problem deserves a rule.”

Ms. McCarthy said Mr. Obama had handed her an epic challenge in his address on climate change at Georgetown University in June. He said that in the face of resistance and inaction in Congress, he would use his executive authority to begin to rein in the emissions that are contributing to global warming. The most meaningful of those powers reside in the E.P.A., which will write regulations governing carbon emissions from power plants, the source of roughly 40 percent of the nation’s greenhouse gas pollution.

Under the president’s timetable, the first of those rules, covering new fossil fuel plants, is due Sept. 20. The agency must produce draft standards for existing plants, a vastly more complex and controversial undertaking, by next June.

“We worked with him on the schedule,” Ms. McCarthy said, referring to the president. “He impressed on us how important it was to get started now. He said to get it done, and get it done right.”

Those rules will require a shift in power generation from coal to cleaner-burning natural gas, or development of new cost-effective means of capturing and storing carbon dioxide emissions. The regulations, along with proposed new rules governing coal-mining waste and the disposal of coal ash from power plants, are what Mr. Manchin and others mean when they say the E.P.A. is waging a war on coal.

Ms. McCarthy rejected the charge.

“We don’t have a war on coal,” she said. “We’re doing our business, which is to reduce pollution. We’re following the law.”