Together with a small group of political appointees, many with backgrounds, like his, in Oklahoma politics, and with advice from industry lobbyists, Mr. Pruitt has taken aim at an agency whose policies have been developed and enforced by thousands of the E.P.A.’s career scientists and policy experts, many of whom work in the same building.
“There’s a feeling of paranoia in the agency — employees feel like there’s been a hostile takeover and the guy in charge is treating them like enemies,” said Christopher Sellers, an expert in environmental history at Stony Brook University, who this spring conducted an interview survey with about 40 E.P.A. employees.
Such tensions are not unusual in federal agencies when an election leads to a change in the party in control of the White House. But they seem particularly bitter at the E.P.A.
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 Steve J. Milloy, a member of Mr. Trump’s E.P.A. transition team and author of the book “Scare Pollution: How and Why 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.”
Mr. Ruckelshaus said such secrecy could pave the way toward, or exacerbate, another disaster like the contamination of public drinking water in Flint, Michigan, or the 2014 chemical spill into the public water supply in Charleston, W.Va. — while leading to a dearth of information when such incidents happen.
“Something will happen, like Flint, and the public will realize they can’t get any information about what happened or why,” he said.
But Liz Bowman, a spokeswoman for the E.P.A., categorically denied the accounts employees interviewed for this article gave of the secrecy surrounding Mr. Pruitt.
“None of this is true,” she said. “It’s all rumors.”
She added, in an emailed statement, “It’s very disappointing, yet not surprising, to learn that you would solicit leaks, and collude with union officials in an effort to distract from the work we are doing to implement the president’s agenda.”
Mr. Pruitt’s efforts to undo a major water protection rule are one example of his moves to quickly and stealthily dismantle regulations.
The rule, known as Waters of the United States, and enacted by the Obama administration, was designed to take existing federal protections on large water bodies such as the Chesapeake Bay and Mississippi River and expand them to include the wetlands and small tributaries that flow into those larger waters.
It was fiercely opposed by farmers, rural landowners and real estate developers.
The original estimate concluded that the water protections would indeed come at an economic cost to those groups — between $236 million and $465 million annually.
But it also concluded, in an 87-page analysis, that the economic benefits of preventing water pollution would be greater: between $555 million and $572 million.
E.P.A. employees say that in mid-June, as Mr. Pruitt prepared a proposal to reverse the rule, they were told by his deputies to produce a new analysis of the rule — one that stripped away the half-billion-dollar economic benefits associated with protecting wetlands.
“On June 13, my economists were verbally told to produce a new study that changed the wetlands benefit,” said Elizabeth Southerland, who retired last month from a 30-year career at the E.P.A., most recently as a senior official in the agency’s water office.
“On June 16, they did what they were told,” Ms. Southerland said. “They produced a new cost-benefit analysis that showed no quantifiable benefit to preserving wetlands.”
Ms. Southerland and other experts in federal rule-making said such a sudden shift was highly unusual — particularly since studies that estimate the economic impact of regulations can take months or even years to produce, and are often accompanied by reams of paperwork documenting the process.
“Typically there are huge written records, weighing in on the scientific facts, the technology facts and the economic facts,” she said. “Everything’s in writing. This repeal process is political staff giving verbal directions to get the outcome they want, essentially overnight.”
Jeffrey Ruchs, the executive director of Public Employees for Environmental Responsibility, an organization representing government employees in environmental fields, said the E.P.A. could not allow changes like this to take place, or expect its employees to follow such directives.
“This is a huge change, and they made it over a few days, with almost no record, no documentation,” Mr. Ruchs said, adding, “It wasn’t so much cooking the books, it was throwing out the books.”
Experts in administrative law say such practices skate up to the edge of legality.
While federal records laws prohibit senior officials from destroying records, they could evade public scrutiny of their decision-making by simply not creating them in the first place.
“The mere fact they are telling people not to write things down shows they are trying to keep things hidden, said Jeffrey Lubbers, a professor of administrative law at American University.
Mr. Pruitt had a reputation for being secretive before he ever came to the E.P.A.
While serving as Oklahoma’s attorney general, he came under criticism for maintaining at least three separate email accounts, including one private email account that he at times used for state government business.
During his Senate confirmation, he was asked about these multiple accounts, providing what some senators considered a misleading answer.
A subsequent lawsuit resulted in the release of some of these other emails, which Mr. Pruitt had asserted did not exist.
“He’s got a serious problem because of his emails down in Oklahoma — he’s burned himself,” said David Schnare, who worked at the agency from 1978 to 2011 and then on the Trump administration’s E.P.A. transition team. “He doesn’t want to take any risks.”
Mr. Schnare, a conservative Republican who has backed President Trump’s broader agenda, had taken on what was expected to be a more permanent role at the E.P.A.
But he resigned from the agency last month in protest of what he said is Mr. Pruitt’s management of the agency.
Mr. Schnare noted that some previous E.P.A. administrators had been secretive — during the Obama administration, for example, Lisa Jackson, the E.P.A. administrator, came under criticism for using an email alias, “Richard Windsor,” to conduct official business.
But Mr. Schnare said that Mr. Pruitt’s methods stood out from all of his predecessors.
“My view was that under this administration we would be good at transparency, particularly in the regulatory area,” he said. “But these guys aren’t doing that.”
Senator Tom Carper of Delaware, the top Democrat on the committee overseeing federal government operations, has criticized Mr. Pruitt for embracing what he calls “a culture of secrecy around everything from his schedule to the way the agency makes scientific determinations.”
Mr. Carper and other Senate Democrats have a dozen outstanding requests awaiting a response from Mr. Pruitt, and when responses do come, Mr. Carper said, they referred lawmakers to printouts of news releases, instead of answering questions.
An E.P.A. spokesman disputed Mr. Carper’s criticisms.
“Administrator Pruitt has responded to 14 of the 27 oversight letters, which often contain numerous in-depth questions and it takes time to provide an extensive and through response,” he said, adding that he “has been incredibly responsive to Congress.”
Mr. Pruitt and his staff are also subject to intense scrutiny from the public and the news media: The E.P.A., just in the last two months, has received more than 2,000 Freedom of Information Requests, many of them focused on Mr. Pruitt, asking for every possible record related to his tenure, including text messages, telephone records and even his web browsing history.
Yet for E.P.A. employees, information about Mr. Pruitt’s activities can be hard to obtain.
In April, for example, he traveled to Chicago to visit an E.P.A.-designated hazardous waste site.
But E.P.A. employees at the agency’s Chicago office said they had no idea he was there — nor did he visit the Chicago branch of the agency, or meet with staff members.
“We learned he was in town when spotted at a Cubs game,” said Nicole Cantello, a lawyer in the E.P.A.’s Chicago office and a leader of the employee union. “But it was treated as a closely guarded secret. He won’t meet with us or talk to us to make decisions about policy, and we don’t even know when he’s in town.”