Mr. Elmendorf said the university had extended the fellowship to Ms. Manning, who was sentenced to 35 years in prison for providing classified information to WikiLeaks, because she fit the Kennedy School’s tradition of asking influential people to address students.
While the school is revoking the title of visiting fellow for Ms. Manning, she is still invited to spend a day at the school and speak at a forum, the dean said.
Ms. Manning commented on the development in a set of early morning tweets, writing that she was “honored” to be disinvited and that the institution was chilling “marginalized voices under C.I.A. pressure.”
In another tweet, she contrasted herself with former Trump staffers like Mr. Spicer and Corey Lewandowski, the president’s former campaign manager, who was also named a visiting fellow.
Chase Strangio, a lawyer for Ms. Manning, wrote in a statement that the decision to withdraw the invitation “in the middle of the night without coherent explanation is disgraceful even for Harvard” and also accused the school of being beholden to the C.I.A.
The decision by the Kennedy School followed forceful denunciations by a former top official at the C.I.A. and the current director at the agency.
Michael J. Morell, a deputy director at the intelligence agency under President Barack Obama, resigned as a fellow on Thursday, calling the invitation to Ms. Manning “wholly inappropriate.” He said 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 Mr. Elmendorf. The letter was obtained and reported on by CBS News, where Mr. Morell is a national security contributor.
Mr. Morell did not respond to an email Thursday night, and the Kennedy School did not respond to a request for comment.
Later on Thursday, the director of the C.I.A., Mike Pompeo, withdrew from a Harvard forum he was scheduled to participate in that night, citing Ms. Manning’s fellowship as the reason.
“Ms. Manning betrayed her country,” Mr. Pompeo, who graduated from Harvard Law School, wrote in a letter to a Kennedy School official, adding that he commended Mr. Morell’s decision to resign.
He added, “It has everything to do with her identity as a traitor to the United States of America and my loyalty to the officers of the C.I.A.”
Ms. Manning was convicted in 2010 for giving WikiLeaks hundreds of thousands of classified diplomatic cables and military reports from the wars in Afghanistan and Iraq. Mr. Obama commuted her sentence in January as one of his final acts as president, and she was released in May.
Since 2013, Mr. Morell had served as a nonresident senior fellow at the Belfer Center for Science and International Affairs, which is also part of the Kennedy School. In his letter, Mr. Morell said he worried that Ms. Manning’s actions would “encourage others to leak classified information as well.”
“I have an obligation to my conscience,” he wrote.