The university’s investigations did not substantiate some other complaints, including ones accusing Mr. Fryer of retaliation.

Mr. Fryer repeatedly told a university investigator that he was being unfairly scrutinized, at one point asking if he was being singled out for his skin color, though some of the accusers were minority women. He explained his “tackle, bite u or both” message as a “same-race thing” with an assistant who was black. The woman told the investigator that the comment was “not a thing that black people say to one another,” in her experience.

At another point, Mr. Fryer asked the investigator to analyze all emails sent from Harvard professors over the last two decades, “to ensure there are no undocumented policy violations according to the standard to which I am being held.”

One of his accusers also filed a complaint with the Massachusetts Commission Against Discrimination, but withdrew it in February because she had reached a “satisfactory settlement” with Harvard. The terms of that settlement have not been made public.

Mr. Fryer came to prominence as part of a new wave of researchers using rigorous empirical methods to tackle social issues beyond traditional economics. Much of his research has focused on the causes of racial achievement gaps in education, and how to close them. Mr. Fryer has put some of his ideas into practice: As chief equality officer for New York City’s Department of Education under Mayor Michael Bloomberg, he spearheaded a pilot program that paid low-income students for earning good test scores.

Mr. Fryer received tenure at age 30, received a MacArthur “genius grant” in 2011, and in 2015 was given the John Bates Clark Medal , which honors an American under 40 for “a significant contribution to economic thought and knowledge.” His Harvard salary was more than $600,000, the university’s 2016 tax filing shows.

Profiles emphasized his rise from a rough childhood in Florida and Texas. He won a scholarship to the University of Texas, Arlington, and graduated in two and a half years before earning an economics doctorate from Penn State.