Earlier, in a brief interview, Ms. Sanders said that Mr. Pruitt’s success in achieving items on the president’s agenda — including rolling back a large number of environmental regulations — may weigh heavily as a counterbalance to allegations that he misused taxpayer dollars.
“He likes the work product,” she said of Mr. Trump.
Conservatives have, for the most, part rallied around Mr. Pruitt, but late Friday saw the first signs of a fissure.
Representative Trey Gowdy, Republican of South Carolina and the chairman of the House Oversight Committee, has started to investigate Mr. Pruitt’s condo deal, an aide to the committee confirmed.
Mr. Gowdy is already investigating Mr. Pruitt’s first-class travel. This week, the committee was provided two memos from the E.P.A.’s designated ethics official related to the administrator’s living arrangements, the aide said.
Asked about Mr. Pruitt at an event on Friday evening, Mr. Gowdy said, “I don’t have a lot of patience for that kind of stuff. You’ve got to be a good steward of taxpayer dollars,” according to a video an activist took of the interaction that was distributed by Friends of the Earth, an environmental group.
Mr. Pruitt has been dogged by a series of scandals in recent weeks, including revelations that he rented a condominium co-owned by the wife of an energy lobbyist for $50 per night; that he spent more than $100,000 on taxpayer-funded first-class travel, which the E.P.A. has argued was necessary because of security concerns; and that the agency sidelined or demoted at least five high-ranking agency employees who had raised questions about his spending.
The Wall Street Journal first reported Mr. Kelly’s unheeded advice to Mr. Trump, which marked the escalation of a quiet, but intense, turn in the West Wing against Mr. Pruitt. Privately, many senior White House aides have become infuriated with the E.P.A. chief and exasperated with his ethical lapses, believing that it is only a matter of time before his special standing with the president wears thin.
But Mr. Trump’s decision to keep Mr. Pruitt in his job over the counsel of his chief of staff also raised new questions about Mr. Kelly’s power in the West Wing. It was only two months ago that Mr. Trump was musing privately about replacing Mr. Kelly in the aftermath of the scandal surrounding Rob Porter, Mr. Trump’s staff secretary who resigned under pressure after it emerged that he had faced allegations of spousal abuse by two former wives.
In recent days, Mr. Trump has appeared determined to do things his own way, and he has conducted a purge of people in his administration who had clashed with him, including Rex W. Tillerson, the secretary of state, and Lt. Gen. H. R. McMaster, the national security adviser whose last day at the White House was Friday.
But Mr. Trump regards Mr. Pruitt warmly, and — for now — has continued to back him.
“I think he’s done a fantastic job at E.P.A.,” Mr. Trump told reporters on Thursday on Air Force One as he returned to Washington from an event in West Virginia. “I think he’ll be fine.”
On Friday, Mr. Trump pushed back against news reports that he had considered replacing Jeff Sessions, the attorney general, with Mr. Pruitt, saying in a tweet that his E.P.A. chief “is doing a great job but is TOTALLY under siege.”
That came hours before yet another embarrassing revelation on Friday afternoon, when Politico reported that the lobbyists who owned the condominium Mr. Pruitt paid $50 a night to rent had leased the space to him for only six weeks, and became frustrated when he declined for months to leave, eventually pushing him out and changing the locks.
The president, who dislikes direct personal confrontations, has been known to change his mind and tone rapidly when it comes to personnel decisions as events unfold and he gauges the reaction in the news media and the potential for damage to his own reputation. But his aides also point out that Mr. Trump relishes doing things his own way and bristles against being told he must adhere to certain conventions, even when failing to do so may mean enduring political fallout.
In interviews in recent days with conservative news outlets, including Fox News and The Washington Examiner, Mr. Pruitt pushed back hard against accusations that his actions were unethical. In an interview with Fox News, he described his living arrangement as an “Airbnb situation,” and said the E.P.A.’s ethics office had signed off on it.
The ethics office ruled that Mr. Pruitt’s condo rental did not violate the agency’s rules. A later memo released this week said the office did not have all the facts about the rental when it made its initial ruling, including reports that Mr. Pruitt’s daughter, McKenna Pruitt, lived at the apartment when she was a White House intern.
Asked by Fox whether renting a room from a Washington lobbyist violated Mr. Trump’s credo of draining the swamp, Mr. Pruitt replied, “I don’t even think that’s even remotely fair to ask that question.”
Mr. Trump, an avid Fox viewer who puts great stock in TV performances, did not appear to think much of Mr. Pruitt’s appearance. Asked Thursday on Air Force One what he thought about it, he paused, smiled wryly and said, “It’s an interesting interview.”
On Friday, a coalition of 64 House Democrats called for Mr. Pruitt’s resignation. Mr. Pruitt’s conservative allies said that is more likely to bolster the administrator’s standing than hurt it and said they hope Mr. Kelly will not force him out.
“If he doesn’t weather this, no one is ever going to take another job in this administration, and John Kelly is an idiot,” said Michael McKenna, a Republican energy lobbyist, adding, “If this turns into a referendum on who is doing more for the president’s agenda, Pruitt will win.”
Conservatives have rallied around Mr. Pruitt. The Wall Street Journal’s editorial page said the E.P.A. chief was being hounded because of his success in dismantling Obama-era environmental standards. Other conservative groups have accused the news media of campaigning for Mr. Pruitt’s ouster.
Mr. Kelly and Mr. Pruitt have clashed in the past. The chief of staff stepped in last year to block an effort by the E.P.A. chief to announce public “red team, blue team” hearings on climate change, an idea that Mr. Pruitt had personally pitched to the president as a way of challenging the science behind global warming. Mr. Trump liked the idea, officials said, but his administration regarded it as foolish at best and potentially disastrous, fearing it could become a spectacle that would undermine the president’s antiregulatory push.
At a December meeting to discuss Mr. Pruitt’s plan, a deputy of Mr. Kelly’s said the plan was “dead” and not to be discussed further.
An earlier version of this article misstated in one instance the amount of money Scott Pruitt paid to rent a condominium co-owned by the wife of an energy lobbyist. It was $50 a night, not $50 a month.
An earlier version of this article misstated the day on which 64 House Democrats called for Scott Pruitt’s resignation. It was Friday, not Thursday.