Deborah Dugan, the suspended chief of the Recording Academy, the organization behind the Grammy Awards, said in a complaint to the Equal Employment Opportunity Commission on Tuesday that she had been removed as retaliation for uncovering a range of misconduct at the academy, including sexual harassment, improper voting procedures and conflicts of interest among academy board members.

Ms. Dugan’s 44-page complaint details her clash with a number of powerful men at the academy during her tenure of just five months. But her accusations also represent an indictment of the academy itself, which has struggled to reform its reputation after coming under harsh criticism for its poor record recognizing women and people of color in the major categories.

The document, filed with the E.E.O.C.’s Los Angeles office and technically called a charge of discrimination, alleges that Ms. Dugan’s predecessor, Neil Portnow, had been accused of rape by an artist, and that the academy’s board had been scheduled to vote for a bonus for him even though all of its members had not been told about the accusation. The complaint has little detail about the accusation, but said that a psychiatrist had said that the encounter was “likely not consensual.”

It also says that Ms. Dugan herself had received unwanted sexual advances from Joel Katz, a powerful industry lawyer who represents the Grammys.