At the apex of the Nigerian Prisons Service sits the Controller-General of the Nigerian Prisons Service. He is the Chief Executive Officer and is responsible for the formulations and implementation of penal policies in Nigeria. He is responsible to the President through the Minister of Interior and the Civil Defence, Fire, Immigration and Prisons Services Board which the Minister heads. But in matters of prison policy he takes direct responsibility for policy implementation.
He is assisted by six (6) Deputy Controllers-General (DCGs) who head the six broad administrative divisions called Directorates into which the Service is broken for efficient management.

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The Deputy Controllers-General who head the Directorates report to the Controller-General and constitute together with the Controller-General the highest decision-making body in the Administration of the Nigerian Prisons Service.
The Directorates are specialized divisions charged with the responsibility of coordinating specific areas of prison administration. They are:

Operations
Administration and Supplies
Health and Social Welfare
Finance and Budget
Inmates’ Training and Productivity
Works and Logistics