Wendy Cleland-Hamnett, the E.P.A. official at the time who ran the office in charge of toxic chemicals and pesticides, said the sudden change in regulatory philosophy was part of a broader trend across the government after Mr. Trump’s election.

“It is certainly similar to the pattern we saw in toxic chemicals as well, where the regulated industry had a more sympathetic ear in the new administration,” said Ms. Hamnett, who left the E.P.A. in late 2017, after a 38-year career with the agency. “And that resulted in a shift in approach as to how these issues would be handled.”

Gary Frazer, the top endangered species official at the Fish and Wildlife Service, whose schedule says he participated in all nine of the late 2017 discussions with Mr. Bernhardt, and who subsequently directed his staff to revise the study, said he did not believe the change in direction was politically driven.

“It was an entirely appropriate role,” he said in an interview, as two of the agency’s public affairs officials listened in. “There was no arm-twisting of any kind.”

The endangered species review is required as part of the re-registration of pesticides, a process that occurs every 15 years.

Experts at the Fish and Wildlife Service and the Commerce Department’s National Marine Fisheries Service were supposed to determine if any of the pesticides might “jeopardize the continued existence of any endangered species or threatened species or result in the destruction or adverse modification of habitat of such species,” a standard created under federal law.

Much of the work focuses on questions like whether a wildfire management program in the Florida Everglades hurt endangered species such as the American crocodile or the West Indian manatee. The Fish and Wildlife Service rarely makes so-called jeopardy findings; a 2015 study of nearly 7,000 cases found that only two concluded with a finding that a species was in jeopardy.