When an allegation of misconduct involves federally sponsored research and the allegation has been made directly to the sponsoring agency, it may conduct its own investigation. Most often, however, the agency will direct the allegation to the home institution for the inquiry and investigation phase, and then accept findings made by the university during its own investigation if necessary. The agency may decide to conduct its own investigation when it believes the home institution is not prepared to handle the investigation in accordance with procedures outlined in federal policies and regulations.

In either case, a sponsoring agency will have substantial involvement by reviewing reports of the inquiry and investigation. In cases where allegations of misconduct involve Public Health Service funds (i.e., National Institutes of Health, Administration for Families, Children and Youth, and other sponsoring agencies in the Department of Health and Human Services), the Office of Research Integrity will serve as the oversight agency. ORI will review and examine reports of proceedings, source data, and documentation, including but not limited to its analysis, grant applications, publications, computer files, letters, and transcripts. This oversight of the investigation assists the agency in determining if the university’s findings are well supported by the evidence and are a defensible final resolution of the allegation.

In cases where the agency accepts a university finding that misconduct occurred, it may still take administrative action. Administrative action can include debarring a person from applying for federal funds for a specified period of time, restricting a person's ability to serve as a principal investigator on a federal grant, or requiring that the person be supervised in his or her work.