Allies of Mr. Pruitt say he is justified in his measures to ramp up his secrecy and physical protection, given that his agenda and politics clash so fiercely with those of so many of the 15,000 employees at the agency he heads.

“E.P.A. is legendary for being stocked with leftists,” said Steven J. Milloy, a member of Mr. Trump’s E.P.A. transition team and author of the book “Scare Pollution: Why and How to Fix the E.P.A.” “If you work in a hostile environment, you’re not the one that’s paranoid.”

Mr. Pruitt’s penchant for secrecy is reflected not just in his inaccessibility and concern for security. He has terminated a decades-long practice of publicly posting his appointments calendar and that of all the top agency aides, and he has evaded oversight questions from lawmakers on Capitol Hill, according to the Democratic senators who posed the questions.

His aides recently asked career employees to make major changes in a rule regulating water quality in the United States — without any records of the changes they were being ordered to make. And the E.P.A. under Mr. Pruitt has moved to curb certain public information, shutting down data collection of emissions from oil and gas companies, and taking down more than 1,900 agency webpages on topics like climate change, according to a tally by the Environmental Defense Fund, which did a Freedom of Information request on these terminated pages.

William D. Ruckelshaus, who served as E.P.A. director under two Republican presidents and once wrote a memo directing agency employees to operate “in a fishbowl,” said such secrecy is antithetical to the mission of the agency.

“Reforming the regulatory system would be a good thing if there were an honest, open process,” he said. “But it appears that what is happening now is taking a meat ax to the protections of public health and environment and then hiding it.”