The decree provides for the commission's "governing council" to have sixteen members, usually known as commissioners in other countries: a chairman, who is to be a retired justice of the supreme court or court of appeal or a retired judge of the high court; representatives of the ministries of justice, foreign affairs and internal affairs; three representatives of registered human rights organizations; two legal practitioners; three representatives of the media, at least two of them from the private sector; three other persons from a variety of interests; and the executive secretary of the commission. None of the current council members have a track-record as human rights activists or critics of military government.

Despite the provision that among the members of the commission's governing council there shall be three members of registered human rights organizations, there was no consultation with Nigeria's human rights groups (many of which are unregistered, because of the difficulty of obtaining registration under a military government) in setting up the commission. The Civil Liberties Organisation, the longest established nongovernmental human rights group in the country, disclaimed any knowledge of Kunle Fadipe, the commissioner alleged to have been nominated to represent it.

The members of the governing council and the executive secretary are appointed by the president, on the recommendation of the attorney-general of the federation, with no further requirement to consult (Section 3(b)). Although it is stated that these individuals shall be "persons of proven integrity" (Section 3(a)), their independence is undermined by the decree's provision that a member of the governing council "may be removed from office by the Head of State, Commander-in-Chief of the Armed Forces, if he is satisfied that it is not in the interest of the public that the member should remain in office" (Section 4(2)). The executive secretary holds office for a five year term and may be reappointed once; the other council members hold office for a term of four years, also renewable once. Only the executive secretary of the council is a salaried position; the other members of the council are paid daily allowances when they are on commission business.

The council hires the staff of the commission directly, and determines their conditions of employment. The commission has four departments: planning, research and statistics (fifteen staff carrying out the substantive work), legal (nine staff), public affairs (six), and administration (fifteen). Other employees are junior support staff.168 Those employees carrying out substantive work have a first degree in law, social sciences and humanities; though most of them have little or no previous experience in human rights work. Some in-house training has been provided, and some members of staff have traveled to attend courses outside the country. The commission is aiming to establish six zonal offices to ensure greater coverage of complaints from around the country, but only those in Lagos and Kano are in place.