The interim president of Columbia University abruptly left her post Friday evening as the school confronted the loss of hundreds of millions of dollars in federal funding and the Trump administration’s mounting skepticism about its leadership.

The move came one week after Columbia bowed to a series of demands from the federal government, which had canceled approximately $400 million in essential federal funding, and it made way for Columbia’s third leader since August. Claire Shipman, who had been the co-chair of the university’s board of trustees, was named the acting president and replaced Dr. Katrina Armstrong.

The university, which was deeply shaken by a protest encampment last spring and a volley of accusations that it had become a safe haven for antisemitism, announced the leadership change in an email to the campus Friday night. The letter thanked Dr. Armstrong for her efforts during “a time of great uncertainty for the university” and said that Ms. Shipman has “a clear understanding of the serious challenges facing our community.”

Less than a week ago, the Trump administration had signaled that it was satisfied with Dr. Armstrong and the steps she was taking to restore the funding. But in a statement on Friday, its Joint Task Force to Combat Antisemitism said that Dr. Armstrong’s departure from the presidency was “an important step toward advancing negotiations” between the government and the university.

The statement included a cryptic mention of a “concerning revelation” this week, which appeared to refer to comments from Dr. Armstrong at a faculty meeting last weekend. According to a faculty member who attended, Dr. Armstrong and her provost, Angela Olinto, confused some people when they seemed to downplay the effects of the university’s agreement with the government. A transcript of the meeting had been leaked to the news media, as well as to the Trump administration, according to two people familiar with the situation.

Ms. Shipman, a journalist with two degrees from Columbia, is taking charge of one of the nation’s pre-eminent universities at an extraordinarily charged moment in American higher education.

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