The commission has been mainly funded by the Nigerian government, from the federation account. Allocated 20 million Naira [approximately U.S.$200,000] in September 1996, the commission received a total of 126 million [U.S.$1,260,000] in 1997, 272 million [U.S.$2,720,000] in 1998, and 101 million [U.S.$1,010,000] for the first three months of 1999.177 The commission has collaborated with international nongovernmental organisations, such as Penal Reform International (sourcing European Union funds) and the Danish Centre for Human Rights, which have funded programs co-sponsored by the commission and national NGOs.

There has been no assistance from the U.N. to the Nigerian Human Rights Commission either before or after the May 1999 handover to civilian rule. The commission did make some requests for assistance both under General Abacha and the transitional government of General Abubakar, but the Office of the High Commissioner for Human Rights had been reluctant to engage with the body under a military government. General Obasanjo traveled to Geneva and met with U.N. High Commissioner for Human Rights Mary Robinson while still president-elect, but this contact has not been built upon since he became head of state.

Adopting a resolution on Nigeria in April 1999, the U.N. Commission on Human Rights, while terminating its consideration of the situation of human rights in Nigeria, called upon the Nigerian government to enhance the independence and effectiveness of the national human rights commission, and requested the Office of the U.N. High Commissioner for Human Rights to respond positively to requests for technical assistance in the field of human rights. Yet the Office of the U.N. High Commissioner for Human Rights, to its frustration, received no request from the Nigerian government or directly from the Human Rights Commission for technical assistance since the inauguration of President Obasanjo, although the offer has been made several times through the Nigerian mission to the U.N. in Geneva. "We've been on standby to give assistance," Ireneo Namboka, desk officer for Nigeria at the Office of the U.N. High Commissioner for Human Rights, commented to Human Rights Watch, "but, surprisingly, we have heard nothing."178 The commission itself has discussed the possibilities for U.N. assistance with the minister of foreign affairs, who was reportedly enthusiastic, but delays internal to the government have apparently meant that no formal approach has yet been made to the Office of the U.N. High Commissioner for Human Rights.179