Internal Affairs should conduct all serious administrative investigations, including but not limited to officer-involved shootings, in-custody deaths, alleged constitutional violations, allegations of racial profiling or discriminatory policing or racial prejudice, dishonesty, drug use, sexual misconduct, cases handled for other jurisdictions, interagency cases, and cases referred directly by the agency head or command staff. Internal Affairs should also conduct all administrative investigations of allegations of misconduct that are likely to result in litigation against the agency or its members. Unless there is a specialized unit to handle internal complaints by employees of discrimination, sexual harassment, and other unlawful employment practices, Internal Affairs should conduct such investigations.
Internal Affairs may investigate instead of the direct supervisor because some policies are set up that way. Internal Affairs can investigate without any feelings being involved towards the officer. When you work together and especially with your direct supervisor they will develop feelings toward you in one way or another whether they like you or not then if they do an investigation their feelings might decide on how the investigation goes.
Internal Affairs are the best ones to do an investigation because this makes sure that everything
Cited: U.S Department of Justice Office of Community Oriented Policing Services http://www.cops.usdoj.gov/Publications/e060930210-InternalAffairs.pdf