None were given any reason for their dismissals, although Mr. Kennedy and Ms. Kenney had been reprimanded by Trump transition officials for answering basic logistical questions from Nikki R. Haley, President Trump’s pick as United Nations ambassador. Mr. Tillerson is widely believed to dislike Ms. Haley, who has been seen as a possible successor if Mr. Tillerson steps down.

In the following months, Mr. Tillerson launched a reorganization that he has said will be the most important thing he will do, and he has hired two consulting companies to lead the effort. Since he decided before even arriving at the State Department to slash its budget by 31 percent, many in the department have always seen the reorganization as a smoke screen for drastic cuts.

Mr. Tillerson has frozen most hiring and recently offered a $25,000 buyout in hopes of pushing nearly 2,000 career diplomats and civil servants to leave by October 2018.

His small cadre of aides have fired some diplomats and gotten others to resign by refusing them the assignments they wanted or taking away their duties altogether. Among those fired or sidelined were most of the top African-American and Latino diplomats, as well as many women, difficult losses in a department that has long struggled with diversity.

One of them was Linda Thomas-Greenfield, a career Foreign Service officer who served as ambassador to Liberia under Mr. Bush and as director general of the Foreign Service and assistant secretary for African affairs during the Obama administration. Ms. Thomas-Greenfield was among those asked to leave by Mr. Tillerson’s staff, but she appealed and remained until her retirement in September.

“I don’t feel targeted as an African-American,” she said. “I feel targeted as a professional.”

For those who have not been dismissed, retirement has become a preferred alternative when, like Mr. Miller, they find no demand for their expertise. A retirement class that concludes this month has 26 senior employees, including two acting assistant secretaries in their early 50s who would normally wait years before leaving.

Image Bill A. Miller, the department’s former chief of security. Credit... U.S. State Department

The number of those with the department’s top two ranks of career ambassador and career minister — equivalent to four- and three-star generals — will have been cut in half by Dec. 1, from 39 to 19. And of the 431 minister-counselors, who have two-star-equivalent ranks, 369 remain and another 14 have indicated that they will leave soon — an 18 percent drop — according to an accounting provided by the American Foreign Service Association.