Two of the career officials, Reginald E. Allen and Eric Weese, were moved to jobs where they had less say in spending decisions and less interaction with Mr. Pruitt, the people said. A third career official, John E. Reeder, joined American University as a temporary "executive in residence" after being told by the E.P.A. to find a new job. And a John C. Martin, who served on the security detail, was also removed from the team and had his gun and badge taken away after raising concerns about how Mr. Pruitt's security was being handled.
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A sixth official, Mr. Pruitt's chief of staff, Ryan Jackson, also raised questions about Mr. Pruitt's spending, according to three E.P.A. officials. He remains in his job but is considering resigning, agency officials said. Mr. Jackson came to the agency from the office of Senator James M. Inhofe, Republican of Oklahoma, who like Mr. Pruitt had been a major critic of regulatory moves made under President Barack Obama, and is a prominent climate change skeptic.
Approval was required by the staff officials for certain of Mr. Pruitt's expenditures, and Mr. Allen, Mr. Chmielewski, Mr. Jackson and Mr. Reeder at various points each voiced concerns to Mr. Pruitt directly about his spending, according to the two administration officials.
Neither Mr. Jackson nor any of the five officials who left or were removed after questioning Mr. Pruitt would comment when contacted by The New York Times. Before their reassignments or removals, Mr. Weese was the head of Mr. Pruitt's protective detail, and Mr. Reeder, Mr. Allen and Mr. Chmielewski each served as deputy chief of staff.
The White House declined to comment on Thursday, referring questions to the E.P.A., though Mr. Trump, as he boarded Air Force One, said he had confidence in Mr. Pruitt.
The E.P.A. challenged the assertion that the reassignments were related to objections to spending and other management issues. "We dispute the veracity of the accusations," said Jahan Wilcox, a spokesman for the agency.
The staff tumult comes to light as Mr. Pruitt's stewardship of the agency is under mounting scrutiny. He is the subject of an investigation by the E.P.A.'s inspector general, who is examining some of the spending and security issues. And though President Trump has tweeted some laudatory comments about Mr. Pruitt, the White House confirmed on Wednesday that it was conducting its own examination.
"We're reviewing the situation," Sarah Huckabee Sanders, the White House press secretary, said. "When we have had a chance to have a deeper dive on it, we'll let you know the outcomes of that. But we're currently reviewing that here at the White House."
Several current and former E.P.A. employees said morale at the agency had suffered as they watched the friction play out between Mr. Pruitt and the officials. Christopher Zarba, a career E.P.A. employee who retired in February after leading the agency's scientific advisory boards, said it was well known in the office that Mr. Allen had been sidelined for challenging Mr. Pruitt.
"Brilliant, a natural leader, an off-the-charts-talented guy," Mr. Zarba said of Mr. Allen. "He had to push back on Pruitt on some of the trip and office modification expenses to keep everything legal, and we speculated he might have been removed for that reason."
A senior political appointee, who came to the agency with the Trump administration and works on policy issues, offered a defense of Mr. Chmielewski: "Kevin is one of the most upstanding public servants and nicest all-around people. Just because he stood up to what was clearly a bad idea, they are trying to sabotage the poor guy's reputation."
Mr. Pruitt declined to be interviewed for this article, but he has spoken with conservative media organizations. In those interviews, he has cried foul about a flurry of media reports about his regular first-class travel, his use of an obscure administrative provision to increase the salaries of two favored aides (over White House objections) and his below-market rental agreement for accommodations in Washington with an energy lobbyist whose clients won favorable treatment from the E.P.A.
The disclosures, he has suggested, were the handiwork of critics who were resorting to personal attacks to derail the deregulatory agenda being pursued by his agency and the Trump administration. Since taking the administrator's job in February 2017, Mr. Pruitt has advanced one of the administration's most aggressive regulatory rollbacks, including regulations intended to tighten rules related to coal-burning power plants, oil and gas drilling, auto and truck air emissions, and pesticides.
Yet the revelations about his staff turnover, which have not been previously reported, demonstrate that concerns about his spending and leadership resonated within his own team well before they became the subject of media reports and investigations by the E.P.A. inspector general and the White House.
Agency records obtained through open-records requests show the critical role that Mr. Allen, Mr. Chmielewski and Mr. Reeder played in reviewing Mr. Pruitt's travel plans. In some instances, several agency officials said, pushback by the officials prevailed.
For instance, in a conversation with one of Mr. Pruitt's closest aides, Mr. Chmielewski sharply objected to a proposal to buy a $100,000-a-month charter aircraft membership that would have allowed Mr. Pruitt to take unlimited private jet trips for official business, according to two administration officials. The membership was not purchased.
Mr. Chmielewski also objected to a proposal to spend about $70,000 to replace two desks in Mr. Pruitt's office suite, including his personal desk and one at a security station outside his office. Asked about the proposed desk purchases, Mr. Wilcox, the E.P.A. spokesman, said that "the administrator never considered the proposal." Pasquale Perrotta, who became head of Mr. Pruitt's security detail after Mr. Weese was removed, insisted that the security desk be upgraded to a bulletproof model, according to current and former E.P.A. employees with direct knowledge of the discussions.
The bulletproof security desk was not purchased, but two new desks were ordered for Mr. Pruitt's personal office: a brown maple wood stand-up desk, with brass locks, that was purchased from a craftsman and an oversize desk with ornate woodworking that had been in a federal government warehouse in Virginia and was refurbished for Mr. Pruitt at a cost of $2,075. E.P.A. employees gawked at the size and grandeur of Mr. Pruitt's refurbished desk, with some comparing it to the Resolute Desk in the Oval Office, officials said in interviews.
Still, Mr. Pruitt and his team obtained many of the perks he wanted. Staff members questioned, but nonetheless approved, frequent trips that routed Mr. Pruitt through hub airports that allowed him to spend weekends at his home in Oklahoma. The administrator also had charter flights approved after they were already taken, the public records show.
"This memorandum responds to your request for written approval for the Administrator and three EPA employees to use a charter service to fly from Denver to Durango, CO on August 4, 2017," read a memo written in late August, after the trip was completed. The approval covered a charter flight to tour the Gold King Mine near Silverton, Colo., after Mr. Pruitt's commercial flight to Denver was delayed. This 40-minute flight cost $5,719, the records show.
Other memos released through the open-records law show that Mr. Allen handled requests for renovations to Mr. Pruitt's office. "I spoke to Gayle and we can proceed as it is not part of the $5,000," read an email to Mr. Allen in April 2017, as staff members were being pressed to find a way to spend more on office renovations than was allowed under federal guidelines. In this case, the expenditure involved a biometric lock and was not counted against Mr. Pruitt's furniture budget. "Approved," Mr. Allen wrote back.
The documents do not reflect the behind-the-scenes friction between Mr. Pruitt and the senior officials, but several agency staff members said in interviews that they avoided putting objections into writing because they suspected there would ultimately be an investigation into the matters.
Mr. Weese, the security official, questioned Mr. Pruitt's desire to use flashing lights and sirens in his motorcade — a perk more commonly associated with the presidency — according to three of the people who worked with or for the E.P.A.
Mr. Pruitt, who often ran late, wanted to use the lights and sirens to expedite local trips in Washington to the airport or to dinner, including at least one trip to Le Diplomate, a trendy French restaurant that he frequented. Such use was not consistent with agency policy, but Mr. Weese was unsuccessful in stopping it.
The agency said Mr. Pruitt played no role in deciding when the sirens and lights would be used. "The security detail for the past 15 years has used them in very limited fashion," the Mr. Wilcox said.
Mr. Weese was also reluctant to sign off on requests for Mr. Pruitt to travel in first class based on security concerns. Mr. Allen, Mr. Chmielewski and Mr. Reeder, too, questioned the use of taxpayer money to pay for first-class airfare. Only after Mr. Weese was replaced by Mr. Perrotta did Mr. Pruitt regularly fly first class, agency staff members said.
There were also questions raised about a request that Mr. Pruitt be issued a bulletproof sport utility vehicle with so-called run flat tires, which keep a vehicle moving even when sustaining gunfire. And they challenged Mr. Pruitt's expanded security detail of approximately 20 members, three times the size of his predecessor's. Unlike his most recent counterpart under Mr. Obama, Gina McCarthy, Mr. Pruitt has security officials follow him wherever he travels, and also stay on duty overnight.
"He wanted to be treated like he was the president," said David Schnare, a prominent conservative lawyer and climate change skeptic, who served on the Trump administration transition team at the E.P.A., after an earlier 30-year stint at the agency that started in the late 1970s.
Mr. Wilcox, the agency spokesman, said the larger security team was justified, given threats against Mr. Pruitt. "They run the variety of direct death threats — 'I'm going to put a bullet in your brain' — to implied threats — 'If you don't classify this particular chemical in this particular way, I'm going to hurt you.'"
There was a particularly intense dispute over a request to construct a special security booth in Mr. Pruitt's office so he could have confidential conversations without being overheard by career agency employees, according to interviews and public documents first reported by The Washington Post.
Mr. Chmielewski suggested converting a broom closet at a cost of about $10,000, one person who worked with the agency said. But Mr. Perrotta wanted a special chamber with sound-dampening privacy products and ceiling baffles that would prevent anyone from intercepting voice or data transmissions. The documents show that the final cost of the new chamber was close to $43,000.
Mr. Perrotta also remains an executive at a private security firm, Sequoia Security Group, which separately received a contract from the E.P.A. to conduct a security sweep of Mr. Pruitt's office, a deal that is also now the subject of an investigation by the agency's inspector general. He did not respond to a request for comment.
The various challenges to Mr. Pruitt's spending and security priorities did not sit well with him, according to the people who worked with or for the E.P.A., and soon the offending aides were removed.
Mr. Allen, a decorated 30-year retired Army officer, was transferred to a different office within the E.P.A., where he mostly works alone, according to two agency officials, one of whom described the setup as "an unmarked grave."
Mr. Weese was transferred from the security detail to a more general position in the agency's criminal investigation division.
Mr. Reeder remains an employee of the E.P.A. while on temporary leave to work at American University. He has been a senior executive at the agency since early in President George W. Bush's presidency, but left for American University after many of his responsibilities were taken away from him.
Mr. Martin, who served on Mr. Pruitt's security detail, raised concerns about Mr. Perrotta and matters related to Mr. Pruitt's security arrangements, such as the soundproof booth. He was then told he could no longer be part of the security detail, which he been a part-time member of for more than a decade, according to two people with knowledge of the events. Mr. Martin then became the target of an inquiry by the agency's inspector general, which ultimately cleared him of wrongdoing, according to documents reviewed by The Times.
The removal of Mr. Chmielewski, the former Trump campaign official, proved more complicated.
As a presidential appointee, Mr. Chmielewski was classified as a member of the senior executive service pay system, and remained in close contact with top aides to both Mr. Trump and Vice President Pence.
Even while at the E.P.A., Mr. Chmielewski helped facilitate trips for Mr. Pence and sometimes traveled with him. And he had a personal connection with Mr. Trump, who had called him to the podium during a campaign rally in April 2016 in Maryland, where Mr. Chmielewski grew up.
"Where the hell is Kevin?" Mr. Trump said at the event. "He's a star. Where is Kevin? Get Kevin up here."
Some internal agency memos detailing Mr. Pruitt's travel plans list Mr. Chmielewski as the coordinator, and as the senior political appointee, he had to ensure that they were properly authorized. Privately, he urged Mr. Pruitt to rein in his spending, initially in person, and then through intermediaries when he got frozen out, according to the two administration officials.
When Mr. Chmielewski returned from a trip to Asia with Mr. Pence in February, he was asked to resign and turn in his credentials. Mr. Pruitt's aides informed the White House that they were dissatisfied with Mr. Chmielewski's unresponsiveness during his travels, including a time when he could not be reached in Hawaii, where he was preparing for a visit by Mr. Pence.
An anonymous complaint filed with the E.P.A.'s inspector general alleged that Mr. Chmielewski could not get the appropriate level of security clearance for his duties because of various indiscretions. After a brief investigation, the inspector general dismissed all the allegations in the complaint as unfounded, according to documents reviewed by The Times.
Mr. Chmielewski told associates that he believed the complaints were an effort by Mr. Perrotta and others to discredit him.
Separately, Mr. Chmielewski also has been the subject of allegations that he was the source of leaks about Mr. Pruitt, and also that he was staying free in the same Capitol Hill home where Corey Lewandowski, Mr. Trump's first campaign manager, lives. Someone familiar with the arrangement acknowledged that Mr. Chmielewski, a longtime friend of Mr. Lewandowski, had slept at the home, but said it was only one night and on a couch.
The crescendo of criticism of Mr. Pruitt has rallied his defenders, including the Tea Party Patriots and the Heritage Foundation, who in recent days have blasted out endorsements of his management of the agency on social media and in opinion columns. It has also empowered his critics, even from within his own Republican Party.
William K. Reilly, who led the E.P.A. under President George Bush, called Mr. Pruitt a "third-rate ideologue" and said he was aware of staff members who had been sidelined at the agency for raising questions about Mr. Pruitt's spending.
"I think he's well beyond his sell-by date," Mr. Reilly said. "Any administration but this one would have discharged him long ago."