“There’s a feeling of paranoia in the agency — employees feel like there’s been a hostile takeover and the guy in charge is treating them like enemies,” said Christopher Sellers, an expert in environmental history at Stony Brook University, who this spring conducted an interview survey with about 40 E.P.A. employees.
Such tensions are not unusual in federal agencies when an election leads to a change in the party in control of the White House. But they seem particularly bitter at the E.P.A.
Allies of Mr. Pruitt say he is justified in his measures to ramp up his secrecy and physical protection, given that his agenda and politics clash so fiercely with those of so many of the 15,000 employees at the agency he heads.
“E.P.A. is legendary for being stocked with leftists,” said Steven J. Milloy, a member of Mr. Trump’s E.P.A. transition team and author of the book “Scare Pollution: Why and How to Fix the E.P.A.” “If you work in a hostile environment, you’re not the one that’s paranoid.”
