The Commission is empowered, to investigate complaints of human rights violations upon receiving submissions from individuals or classes of persons, or on its motion with a view to making recommendations to relevant parties or authorities on effective remedies for such violations or recommending other measures necessary for the effective protection and promotion of human rights

The Complaint Handling System guides complaint handling. Presently, this system is largely manual-based but progress is being made to computerize it. The system process involves receipt, screening and handling of cases. An officer is designated to receive complaints from members of the public who call on the Commission offices in person. The Commission also receives complaints through phone conversations, letters and emails. All complaints must provide details of the one or ones complaining, the complaint, the victim of the complaint as well as the one or ones alleged to have caused the complaint. At this stage, the Commission does not yet open a file

Once a person(s) designated has screened the complaint, usually a lawyer, the Complaint is recommended for action by the appropriate director. Some complaints require that action be escalated to the Executive Secretary, Chairperson of the Commission or the full Commission for decision making on the action to be taken. To aide quality assurance, the Secretariat has established a complaint handling committee, which meets fortnightly

Upon screening, complaints are either rejected for want of merit; advice provided; referred elsewhere with proper jurisdiction or; admitted for further action. Where complaints have been admitted for further action, the complaint is now treated as a case and a case file is opened for such a case. Usually such further actions include investigations, litigation and alternative dispute resolution. In all these processes, the Commission has power to determine its own methods of operations. These include public inquiries and hearings, among others methods. The Commission is also empowered to co-opt any person in the exercise of its powers

During the period, 1998 to 2018, the Commission has handled a total of 4,700 cases. 1,535 of the cases related to civil and political rights, 2,086 related to economic, social and cultural rights, 425 belonged to gender and women rights, 394 related to child rights, and 196 were on disability and elderly rights