“If this were an actually serious policy concern about a state’s performance,” she said, “it’s inconceivable that this wouldn’t be a subject of discussion for months, if not years, between the region and state.”

In fact, according to the latest review of California’s performance under the Clean Water Act, the state’s rate of “significant noncompliance” was below the national average. It also had more stringent pollution limits and tougher monitoring than many other states.

California, the country’s most populous state, does face numerous environmental compliance problems, but E.P.A. officials said many other states have violations at least as serious. California is generally acknowledged to be one of the states that works hardest to resolve its environmental problems.

“California is the place that has innovated more than anywhere else on air pollution and other regulations,” said William K. Reilly, who served as administrator of the E.P.A. under the first President George Bush . “Everybody knows that.”

Mr. Stoker, who is based in Los Angeles, did not attend the all-hands meeting on the day Mr. Wheeler delivered his letter. Instead, it was led by the office’s regional counsel, Sylvia Quast. Other top agency officials, including the director s of the offices of compliance and water, also attended. The regional office has since held at least one other meeting to discuss Mr. Wheeler’s accusations.

The message from the E.P.A.’s leadership in California has been consistent: Mr. Wheeler’s office bypassed the people who know the most about the state and work most closely with state and local officials. The office has been rerouting requests for the data that supports Mr. Wheeler’s accusations to Washington because the San Francisco office does not have it. They have also advised staff members concerned that the letters have undermined the E.P.A.’s working relationship with the state to tell their counterparts at California agencies that the letter is purely political and that the regional office had nothing to do with it.

On Tuesday, two senior E.P.A. officials acknowledged that the concerns expressed in the letter did not originate from the regional office. They also asserted that questions over process and turf should not overshadow genuine problems with California’s air and water quality.