The agency’s biggest civil case filed since Mr. Trump took office involves Exxon Mobil, which was accused of not properly operating and monitoring industrial flares at its petrochemical facilities. Exxon agreed in October to pay $2.5 million in civil penalties, some of which will go to Louisiana, and spend $300 million to install new technology to reduce air pollution.

The agency on Friday also released a list of 21 Superfund sites contaminated with hazardous substances and pollutants that Mr. Pruitt has targeted for immediate and intense attention. One of the sites on the list, Tar Creek, a former lead and zinc mine, is in Oklahoma, where Mr. Pruitt once served as attorney general and state senator.

But more than a dozen current and former E.P.A. officials told The Times that the slowdown in enforcement is real on the ground, and that it is being directed from the top.

At the Ralph Metcalfe Federal Building in Chicago, which houses a regional office of the E.P.A., employees said it has become difficult to even start a new investigation. Because it covers states populated with Rust Belt industries, the Chicago office has traditionally been one of the busiest of the 10 regions.

An agency spokeswoman, in a statement, said “we have not rejected any requests for sampling, monitoring and testing” that were sent to headquarters as a result of the new policy. But agency staff said the memo made clear such requests were discouraged, and many fewer were being drafted.

Jeff Trevino, a lawyer in the Chicago office, who has worked for the agency for 27 years, said the new hurdles imposed by Mr. Pruitt had created “a Catch-22” because, with new policies effectively discouraging requests for information, investigators will have a harder time getting the data needed to detect and confirm violations.

Mr. Trevino, like other current E.P.A. employees, was not authorized by the agency to speak with The Times, and did so as a member of the labor union.