“I got phone calls from conservatives wanting to know, ‘Why did we do anything? Why are we putting forward a proposal at all?’” Mr. Wheeler acknowledged in an interview last week. His argument, that more restrictive replacement is better than killing off the climate regulation entirely, won the day.

Then, in August, the E.P.A. and the Transportation Department moved to gut another major federal effort to combat climate change by relaxing rules aimed at reducing car tailpipe pollution. The Trump administration plan also voided California’s ability to set its own, stricter standards, triggering a potentially ugly legal battle between Washington and blue states over the ability to fight global warming.

Mr. Wheeler, according to several people involved in the discussions, pushed back forcefully against an analysis used by highway officials to justify the rollback, which argued that stricter fuel pollution rules would cause thousands of deaths in road accidents. The agency argued that more efficient cars are less safe because they are lighter .

People who have attended meetings with Mr. Wheeler said he argued that the fatality numbers relied on bad calculations and were likely to be successfully challenged in court.

Mr. Wheeler on Friday denied that he had clashed with Jeffrey A. Rosen, the chief Transportation Department architect of the auto-standards rollback, saying he merely sought to understand his colleagues’ mathematical modeling and legal reasoning. “I wanted to make sure what we were putting forward would be upheld in the courts, and he assured me that the work they had done would be,” Mr. Wheeler said.

A department official, speaking on condition of anonymity because he was not authorized to speak on the record, said o n Tuesday that there was “no dispute” between the agencies.

Mr. Wheeler’s predecessor, Mr. Pruitt, faced more than a dozen federal investigations into his conduct, including his extensive use of first-class air travel, renting a condo from the wife of an energy lobbyist with business before the E.P.A. and enlisting aides on personal tasks like buying a used mattress from Trump International Hotel and seeking a Chick-fil-A franchise for his wife.