The Ghanian government covers the bulk of the funding for the CHRAJ. Article 220 of the Constitution provides that the CHRAJ's budget should be charged to the government's Consolidated Fund and not linked to any one government department. However, in practice, the budget is still subject to the approval of the Ministry of Finance which always cuts the proposed budget after budget hearings. The CHRAJ has recommended that it should present its budget directly to parliament to make its independence more meaningful. Meanwhile, it has depended heavily on foreign donors for support. Foreign donors, including the Danish and British governments and foundations, meet the costs of library facilities, training, computers, and the educational program.

Inadequate funding results in the loss of many CHRAJ-trained personnel to other government agencies who are able to pay their employees more. In November 1998, the CHRAJ submitted a petition on this matter to the government and was still awaiting a response a year later.