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Not all the political appointees will be permitted to stay, but Mr. Morrell declined to identify those asked to leave.

“To the extent you are willing and in a position to continue to serve, I am deeply appreciative,” Mr. Gates stated in the email. “However, I encourage you to continue to prudently plan for the transition from DOD employment, as the pace of personnel decisions by the incoming administration is likely to accelerate.”

Mr. Gates said he could not provide “more clarity and guidance” on how long those that wish to become holdovers will be allowed to stay on in their positions.

The secretary said he appreciated the appointees’ willingness to continue “in the interest of providing continuity for this department and for its critical mission to the nation in a time of war.”

Mr. Gates promised to thank each appointee personally in January. “But I still want to take advantage of this note to thank you collectively for all you have done for our country. I wish you and yours happy holidays,” he said.

The note was signed “Bob Gates” and sent by Mr. Gates’ chief of staff, Robert Rangel.