Mr. Elmendorf told Ms. Manning, who was sentenced to 35 years in prison for providing classified information to WikiLeaks, that she was still invited to speak at Harvard. But he said that the school could no longer give her the title of visiting fellow. The school was concerned that the title implied an endorsement and did not want to come across as endorsing Ms. Manning and her views, he said.

Image Douglas W. Elmendorf, the dean of the Harvard Kennedy School, in August 2014, when he was the director of the Congressional Budget Office. Credit... Alex Wong/Getty Images

When asked by a member of Ms. Manning’s team why Mr. Spicer and Mr. Lewandowski were being endorsed, Mr. Elmendorf said that they had something to bring to the table, the source said.

The call lasted about 10 minutes; Ms. Manning’s team left the conversation stunned and insulted.

The sudden turnabout by the school came after a day of intense backlash over the university’s announcement that Ms. Manning had been included. Mr. Elmendorf said that while the university encouraged a diversity of opinions and did not shy away from controversy, naming Ms. Manning a fellow was a mistake for which he accepted responsibility.

“I see more clearly now that many people view a visiting fellow title as an honorific, so we should weigh that consideration when offering invitations,” he wrote in a letter posted on the Harvard Kennedy School website early Friday morning, shortly after the phone call with Ms. Manning. “I apologize to her and to the many concerned people from whom I have heard today for not recognizing upfront the full implications of our original invitation.”