The allegations were levelled in 2015 against the university by a coalition of 64 Asian-American groups, including four Indian-American organisations.
The New York Times reported that the Trump administration intended to increase the Justice Department's efforts to target universities whose admission policies it deemed discriminatory against white applicants, a report in The Harvard Crimson, a student newspaper of the university, said.
The Justice Department's Civil Rights Division will investigate the allegations.
The Crimson report said that the university has repeatedly and emphatically denied allegations that it uses racial quotas in its admissions process.
A Justice Department spokesperson said the investigation would focus on a single complaint filed in 2015 accusing Harvard in particular of discriminating against Asian-Americans in its undergraduate admissions processes, the Crimson report said.
"The posting sought volunteers to investigate one administrative complaint filed by a coalition of 64 Asian-American associations in May 2015 that the prior administration left unresolved," Justice Department spokesperson Sarah Isgur Flores said in a statement yesterday.
"This Department of Justice has not received or issued any directive, memorandum, initiative, or policy related to university admissions in general," the statement said.
Among the 64 organisations were four Indian-American community associations -- American Society of Engineers of Indian Origin, BIT Sindri Alumni Association of North India, Global Organisation of People of Indian Origin-Los Angeles Chapter and National Federation of Indian American Associations.
The Department of Education had later dismissed the complaint saying it was similar to an ongoing and separate federal lawsuit filed against Harvard.
"To become leaders in our diverse society, students must have the ability to work with people from different backgrounds, life experiences and perspectives. Harvard remains committed to enrolling diverse classes of students," Harvard spokesperson Rachael Dane said.
"Harvard's admissions process considers each applicant as a whole person, and we review many factors, consistent with the legal standards established by the US Supreme Court".
The Class of 2021 is 22.2 per cent Asian-American, a record high for the university, the Crimson report added.
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