In a statement, Ed Chen, a spokesman for the Natural Resources Defense Council, said, “Scientists at the EPA who know something about climate science want nothing to do with the Red Team, Blue Team exercise.”

The emails suggest that E.P.A.’s Office of Research and Development, which does most of the agency’s science work, was not active in the discussions around the debates. In one email, a program analyst in the office, Christina Moody, wrote: “We are not involved. The Administrator is the one who wants to do this and I’m guessing his folks are putting it together.”

A spokesman for the E.P.A., Jahan Wilcox, declined to offer a statement on the emails.

Last December, President Trump’s chief of staff, John F. Kelly, let it be known that the red team, blue team debates should be considered “dead,” according to people familiar with a White House meeting on the matter that month. After that, however, the emails show Mr. Pruitt continued setting up meetings to discuss the broad themes favored by organizations that question climate change, while not explicitly citing the idea of a debate.

“We were thinking this meeting could be purely informative in nature, and not necessarily in the context of a specific EPA exercise,” Tate Bennett, associate administrator at the E.P.A., wrote to Oren M. Cass, a senior fellow at the Manhattan Institute for Policy Research, a conservative think tank, in a Jan. 18 email.

Mr. Cass on Wednesday said his work was focused on the economics of addressing climate change and that he believed the analyses that the E.P.A. and others have used in the past to justify action were flawed.

“I encourage conservatives to accept mainstream climate science and focus on economic analysis and good public policy,” Mr. Cass said.

Mr. Pruitt first publicly floated the idea of having climate science debates — possibly televised — to a group of coal executives last June. And at least a month earlier, in May 2017, the documents show, the E.P.A. staff was working with groups that oppose mainstream science to develop the concept.