Late last year, the E.P.A. sponsored a drive on Facebook and Twitter to promote its proposed clean water rule in conjunction with the Sierra Club. At the same time, Organizing for Action, a grass-roots group with deep ties to Mr. Obama, was also pushing the rule. They urged the public to flood the agency with positive comments to counter opposition from farming and industry groups.

Image Left, a Twitter post from the agency promoting the rule.

The results were then offered as proof that the proposal was popular.

“We have received over one million comments, and 87.1 percent of those comments we have counted so far — we are only missing 4,000 — are supportive of this rule,” Ms. McCarthy told the Senate Environment and Public Works Committee in March. “Let me repeat: 87.1 percent of those one-plus million are supportive of this rule.”

But critics said environmental groups had inappropriately influenced the campaign — just as environmentalists complained that the energy industry improperly drove policy during the George W. Bush administration.

At minimum, the actions of the agency are highly unusual. “The agency is supposed to be more of an honest broker, not a partisan advocate in this process,” said Jeffrey W. Lubbers, a professor of practice in administrative law at the American University Washington College of Law and the author of the book “A Guide to Federal Agency Rulemaking.”

“I have not seen before from a federal agency this stark of an effort to generate endorsements of a proposal during the open comment period,” he said.

Senator James M. Inhofe, Republican of Oklahoma and chairman of the environment committee, is holding a hearing on Tuesday to examine the proposed rule. “There is clear collusion between extreme environmental groups and the Obama administration in both developing and promoting a host of new regulations,” he said.

The most contentious part of the E.P.A.’s campaign was deploying Thunderclap, a social media tool that spread the agency’s message to hundreds of thousands of people — a “virtual flash mob,” in the words of Travis Loop, the head of communications for E.P.A.’s water division.