State officials from California and the other states, including New York, had threatened to sue the E.P.A. in order to get a decision on the waiver, accusing it of dragging its heels. California first approved the regulations in 2003. Two years later, it submitted a request to the E.P.A. to put the standards into effect.

The agency initially argued that it did not have the authority to regulate greenhouse gas emissions under the Clean Air Act. But earlier this year, the United States Supreme Court ruled that the agency could do so.

Gov. Arnold Schwarzenegger of California and the attorney general, Edmund G. Brown Jr., said Wednesday that they were prepared to "sue at the earlier possible moment" to try to force the E.P.A. to allow the state to set emissions standards.

Even if that happens, the states probably would not be able to implement the standards as soon as they had liked. Any legal action might not be settled in time for the regulations to begin taking effect in 2009, as California had hoped.

In recent months, the Bush administration has lost several major court cases over emissions and other environmental standards.

"This decision is like pulling over the fire trucks on their way to the blaze," said Fred Krupp, president of Environmental Defense, which supported the waiver. "For 40 years, E.P.A. administrators have recognized the important role that California plays in innovating new standards to fight pollution."

Automobile companies praised the agency for rejecting the California request. "We commend E.P.A. for protecting a national, 50-state program," said David McCurdy, president of the Alliance of Automobile Manufacturers.