Terry Hartle, a senior vice president at the American Council on Education, a higher education trade group, called the investigation “a taxpayer-funded, politically motivated fishing expedition,” and said it was an unwarranted attack on genuine efforts to recognize and to right the wrongs of history.

“It’s to their great credit that leading universities are asking themselves what they should have done differently in the past, and what they will do differently in the future to be more welcoming and inclusive,” Mr. Hartle said.

The Trump administration declined to comment beyond acknowledging the authenticity of its letter to Princeton, which demanded a response within 21 days. It asked in its letter whether Mr. Eisgruber, when he said that racist assumptions “remain embedded in structures of the university itself,” was acknowledging that Princeton’s assurances to the government and the public that it does not discriminate “have been false and misleading.”

Mr. Eisgruber’s letter cited as an example of systemic racism the fact that “Princeton inherits from earlier generations at least nine departments and programs organized around European languages and culture, but only a single, relatively small program in African studies.”

The investigation follows a series of moves by the Trump administration challenging Ivy League universities. In August, after a two-year investigation of a complaint by a coalition of Asian-American organizations, the Justice Department accused Yale of violating federal civil rights law by illegally discriminating against white and Asian-American applicants.

The department demanded that the university stop considering race or national origin in its next admissions cycle or face a federal lawsuit, and set a deadline of earlier this week for it to comply. Yale declined, but the department had not yet filed suit by Thursday.

Two years ago, the Justice Department publicly backed Asian-American students in a lawsuit accusing Harvard of systematic discrimination. A federal judge ruled in Harvard’s favor last year, but the government has continued to support the plaintiffs, including at a federal appeals hearing on Wednesday.

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