During the period in which General Abacha was head of state the Human Rights Commission's activities were limited by the repressive political environment in which it operated and the conditions under which it was created. The commission issued no criticism of the closely controlled "transition program" put in place by General Abacha, apparently designed to ensure his self-succession as a "civilian" president, nor did it speak out strongly about human rights violations such as the trial and conviction by a special military tribunal of several tens of military officers and civilians for involvement in an alleged December 1997 coup plot.

However, it did carry out some useful work in less controversial areas, particularly in relation to the often life-threatening prison conditions in Nigeria. Human Rights Commission chair Paul Nwokedi told Human Rights Watch: "It is easy to criticize us, but you have to remember the very difficult environment that we are working under. We have tried to make a difference where we can. You may say that we have not addressed the `important' human rights issues, but for a prisoner whose release we have secured from prison our work is important."169 During its first year the commission visited seven prisons, noting in particular severe overcrowding (close to double capacity, at the prisons visited) and the very high proportion of prisoners (74 percent) who were awaiting trial. The commission made recommendations to the government, which established a Committee on Prison Reform and Decongestion, headed by the attorney-general and minister of justice. The work of the committee resulted in the release of several thousand prisoners during 1998 and 1999 and the closure of five prisons on the grounds that they were unfit.170

The commission has also provided some protection to national human rights NGOs, for example, by its sponsorship of seminars and workshops that might have been disrupted while General Abacha was in power had it not been for the endorsement of a government body. The commission designated 1998 a "year of human rights education" and carried out a range of activities for the year, mainly seminars, but including establishing a pilot scheme for "human rights clubs" in secondary schools. The commission publishes a monthly newsletter for the clubs, Human Dignity. The commission also organized or sponsored workshops organized by other groups on a range of human rights issues, including training sessions for prison officials with the International Committee of the Red Cross (ICRC), the prison service and the NGO Prisoners Rehabilitation and Welfare Action (PRAWA)as well as training for lower court judges with the Civil Liberties Organisation and the National Judicial Commission.

On the death of General Abacha in June 1998, General Abdulsalami Abubakar came to power, scrapped the Abacha transition program, and instituted a new one under conditions of greater openness. He progressively released political prisoners and otherwise improved the human rights situation. Soon after General Abubakar assumed power, Justice Nwokedi, chair of the commission, submitted a memorandum urging the government to repeal laws not in conformity with international human rights standards, to ensure government agencies respected court orders, to decongest prisons and police cells and improve conditions, and to ensure that the security forces ceased detaining relatives of suspects in place of the suspects themselves. Nwokedi also called on the president to strengthen the powers of the commission in its enabling legislation and to entrench its position in the new constitution being drafted to take effect on handover to a civilian government.171 Immediately before handing over power, General Abubakar did indeed repeal a range of repressive decrees; however, the human rights commission was not included in the new constitution.

Representatives of the commission have regularly traveled to the sessions of the African Commission on Human and Peoples' Rights, and the commission has a pending application for observer status. Consideration of this application remained delayed as of Feburary 2000 pending the drafting of rules for the status of national human rights institutions before the African Commission. The commission has released a number of publications, including an information brochure about its own activities, a report on prison conditions based on visits carried out in 1997, several editions of a human rights newsletter, and a manual on human rights for prison officers.

Complaints may be lodged with the commission by individuals acting on their own behalf, as representatives of a group, or on behalf of others who cannot act in their own name; or by an association in the interest of its members. The commission attempts amicable settlement of complaints, and failing amicable settlement investigates and makes recommendations to the relevant agency, which may include appropriate sanctions against any person responsible for abuses. Meetings of the commission's council are private, but the council "may, if it deems necessary" allow the complainant to be represented.172 The commission received forty-one complaints in 1996, 114 in 1997, and 172 in 1998. By May 1999, a little over a quarter of these complaints had been disposed of according to rules for admissibility and processing of complaints adopted by the council.173

On May 29, 1999, former military ruler General Olusegun Obasanjo was inaugurated as a civilian president of Nigeria, following elections that took place from December 1998 to February 1999 under the program implemented by General Abubakar. The commission has set out ambitious plans for the future, including on-site investigations of situations where human rights violations are taking place, such as communal conflict; continued monitoring of prison conditions; review of laws in conflict with human rights standards; improving complaint handling; programs for human rights education; and the development of a national action plan for human rights.174 In June 1999 the commission announced the establishment of a 100 million [approximately US$1 million] trust fund to assist victims of human rights violations, including paying for legal and medical assistance.175 In conjunction with the Lagos-based NGO Huri-Laws, the commission is intending to lead the development of a national action plan on human rights, as the South African Human Rights Commission had done. A delegation from the governing council also visited the Niger Delta, met with government and community leaders, and submitted a report to the government on human rights issues arising in connection with unrest in the oil producing region. The commission has submitted proposals to the attorney-general, and met with members of the National Assembly committee dealing with matters related to the judiciary and human rights, concerning the need for new legislation to give the commission the legal powers it needs.176 The government itself has not made clear its attitude to the commission, whether it supports the body in its current form or believes new legislation should be drafted, and the commission reconstituted.