Michael Morell, a former deputy director at the C.I.A., resigned as a fellow at Harvard on Thursday.

A former top C.I.A. official resigned as a fellow at Harvard on Thursday over objections that the university had offered a fellowship to Chelsea Manning, a former United States soldier convicted of leaking classified information.

Michael J. Morell, a deputy director at the intelligence agency under President Barack Obama, called the invitation from the Harvard Kennedy School to Ms. Manning “wholly inappropriate” and said that it “honors a convicted felon and leaker of classified information.”

“It is my right, indeed my duty, to argue that the school’s decision is wholly inappropriate and to protest it by resigning from the Kennedy School,” Mr. Morell wrote to the school’s dean, Douglas W. Elmendorf. The letter was obtained and reported on by CBS News, where Mr. Morell is a national security contributor.

Also on Thursday, the director of the…