Dr. Carlin said he was concerned less about how he had been treated than about what he described as the agency’s unwillingness to hear the arguments of climate change skeptics. He said there was an obvious “imbalance” between the billions of dollars the government had spent building a case for dangerous climate change and the lack of attention to a handful of skeptics like him.

The affair began in March as the E.P.A. was rushing to document the scientific justification for its proposed finding that emissions of carbon dioxide and five other greenhouse gases endangered public health and the environment. The finding was largely an updated version of a similar report, prepared last year under the Bush administration, that came to the same conclusion. But the Bush administration never acted on the research or issued an actual finding.

Image Conservatives say Alan Carlin, a global warming contrarian at the Environmental Protection Agency, was muzzled there. Credit... Stephen Cowley/The New York Times

The agency’s officials were acting in March under severe time constraints to prepare the finding for the E.P.A. administrator, Lisa P. Jackson, who was planning to issue it in mid-April, fulfilling a presidential campaign pledge by Barack Obama. The finding set the stage for the government to regulate greenhouse gases for the first time, an initiative that will resonate through the economy for decades.

Dr. Carlin, long known as a skeptic on global warming, was not invited to submit comments on the document. But he was determined that his views be heard.

He rushed out a 93-page report that cited a variety of sources in raising questions about global warming and the usefulness of government action to combat it. In an accompanying e-mail message to superiors, he said the belief in global warming was “more religion than science” and warned that regulating carbon dioxide would be “the worst mistake that E.P.A. has ever made.”

Agency officials and outside experts who reviewed his report as a result of the outcry over the episode have said they found it wanting in a number of ways. It included unverified information from blog posts, they found, quoted selectively from journal articles, failed to acknowledge contradictory information and may have borrowed passages verbatim from the blog of a well-known climate change doubter.