Federal scientists also say the national study is being used to squelch other research by the E.P.A. on hydrofracking. At a January meeting in Washington, Jeanne Briskin of the E.P.A.’s Office of Research and Development informed regional directors that the national study would be the only forum for research on hydrofracking.

This meant, these scientists said, that some projects under way in regional offices would probably have to be halted.

“That may impact our plans to pursue some of the other research,” wrote Ron Landy, regional science liaison of E.P.A. Region 3, in an e-mail to another agency official in January in which he complained about the new directive.

He suggested that until the directive was lifted, his staff should keep quiet about its continuing hydrofracking research and instead emphasize its work on coal to superiors. “I think we can go ahead, but keep the focus on mining, and prepare for moving these efforts into hydraulic fracking once these limitations are lifted,” Mr. Landy wrote.

Though the E.P.A. has emphasized the importance of openness and public involvement in the study, internal e-mails show agency officials expressing concern about the reaction if the public were to learn of the narrowing scope of the study. In those e-mails, these officials strongly discourage putting anything in writing about the study unless it is vetted by managers.

One e-mail, forwarded to The Times by David Campbell, director of the E.P.A. Region 3 Office of Environmental Innovation, described the instructions he had been given by the agency’s regional administrator, Shawn M. Garvin.

“He could not have been more adamant or clear about the development of any documentation related to our efforts on Marcellus,” Mr. Campbell wrote last December, referring to the Marcellus Shale, a gas-rich rock formation that stretches under Pennsylvania and other states. “His concern is that if we spell out what we think we want to do (our grandest visions) that the public may have access to those documents and challenge us to enact those plans.”