Kash Patel, the F.B.I. director, is pushing ahead with a plan to decentralize the agency’s command structure and divide the bureau into three regions, according to an internal email obtained by The New York Times.

The move will mean that in effect, the top agents in 52 field offices around the country will no longer answer to the deputy director, a significant departure from the way the bureau has done business.

Instead, those field offices will report to three branch directors at headquarters who will be in charge of the East, West and Central regions. The remaining three F.B.I. offices and the largest in the country — New York, Washington and Los Angeles — will answer to the deputy director.

“These changes are meant to empower our S.A.C.s through improved engagement and leadership connections,” said the email, which was sent on Friday, referring to special agents in charge, who typically oversee field offices in a given region.

It represents a shift after a quarter-century of an F.B.I. run under a structure put in place by Robert S. Mueller III after the Sept. 11 attacks. The model was established to address administrative lapses and bolster efforts to deter terrorism. In Mr. Patel’s iteration, he has appointed a total of five branch directors, eliminating the executive assistant directors who previously managed the F.B.I. on a daily basis.

The announced changes were not unexpected, as Mr. Patel has already moved to reduce the number of F.B.I. employees working at headquarters and push them into the field, making good on a pledge he made before becoming director. His efforts have drawn praise from President Trump.