Of the employees who have quit, retired or taken a buyout package since the beginning of the year, more than 200 are scientists. An additional 96 are environmental protection specialists, a broad category that includes scientists as well as others experienced in investigating and analyzing pollution levels. Nine department directors have departed the agency as well as dozens of attorneys and program managers. Most of the employees who have left are not being replaced.

The departures reflect poor morale and a sense of grievance at the agency, which has been criticized by President Trump and top Republicans in Congress as bloated and guilty of regulatory overreach. That unease is likely to deepen following revelations that Republican campaign operatives were using the Freedom of Information Act to request copies of emails from E.P.A. officials suspected of opposing Mr. Trump and his agenda.