The department dismissed the complaints against Dartmouth and Brown because, it said, Mr. Zhao failed to provide sufficient evidence of discrimination at those institutions.

The Justice Department’s Civil Rights Division began investigating Yale’s admissions practices in April of this year, according to the letter. The Education Department joined later based on “information related to a particular Asian-American applicant’s experience applying to Yale,” the department’s letter said.

Yale contends that its admissions process is not intended to create a specific racial mix of students, but rather a student body with a wide variety of ethnic, socioeconomic and other backgrounds. The college said that it takes academic achievement, interests, leadership skills and background into account during the admissions process.

“One goal of Yale’s admissions process — forged through decades of experience and review — is to create a vibrant and varied academic community in which our students interact with people of different backgrounds, experiences and perspectives,” Mr. Salovey said.

Mr. Salovey accused the Justice Department of undertaking the inquiry as part of a larger plan to dismantle affirmative action. “This investigation takes place in the context of legal challenges at other universities aimed at overturning Supreme Court precedent permitting the consideration of race in college admissions,” he said.

Conservative advocates have sought a case to take to the Supreme Court that would challenge schools that take race into account when admitting students, and now they have a more sympathetic administration and the prospect of a conservative majority on the Supreme Court if President Trump’s nominee to the court, Judge Brett M. Kavanaugh, is confirmed.

Mr. Zhao is the president of the Asian American Coalition for Education, a group that has also accused Harvard of using race as a factor to unfairly reject top-performing Asian-American students. The group filed a friend-of-the-court brief in the Harvard lawsuit, accusing the school of discriminating against Asian-American applicants. That trial is scheduled to begin in federal court in Boston on Oct. 15.