UNAFEI operates under the joint auspices of the United Nations and the Government of Japan. UNAFEI' s faculty members are selected from among criminal justice practitioners including a judge, prosecutors, correctional and probation officers. The appointment of the Director of UNAFEI is made in consultation with the United Nations.

Currently, UNAFEI' s annual schedule consists of four multilateral training programmes and several country/region-oriented training programmes held at UNAFEI, Tokyo and a regional seminar for Southeast Asian countries held outside of UNAFEI. In every course and seminar, a different theme focusing on outstanding issues in the field of crime prevention and criminal justice is selected and discussed with due regard to United Nations priority matters and requests from the participating countries. As of 31 March 2011, participants of these training courses and seminars number more than 4,500 from a total of 130 countries and regions (including Japan) and some of them have become top-ranking officials, including Ministers of Justice, Attorneys-General and Chief Justices. The network developed through these training courses and seminars contributes to the mutual co-operation in criminal justice among participating countries including Japan.

Of all of the institutes comprising the United Nations Crime Prevention and Criminal Justice Programme Network (PNI), located in Latin America, Africa, North Europe, etc., UNAFEI has the longest history. UNAFEI continues its contributions to the establishment and implementation of the United Nations policies toward worldwide crime prevention and effective treatment of offenders, keeping close contact with the United Nations Office on Drugs and Crime (UNODC) in Vienna and other PNI.