NISER Act and NISER Medium-Term Strategic Plan 2011-2015 determine the organisational structure of the Institute.

The Institute has a Governing Council, Office of Director-General and departments. There are five departments consisting of three research departments and two non-research departments. Research departments are organised in two working groups each. Non-research departments are organised in divisions and units.

A Director-General, who is the Chief Executive, heads the Institute. Each of the five departments has a Director, while working groups, divisions and units have Heads. The Director-General is assisted in the administration of the Institute by the several committees and boards, including the Management Committee. The Management Committee comprises the Director-General, Directors of Departments – five of them, Head of the Technical Collaboration and Corporate Planning Unit (TCCPU) and a secretary.  The Institute is self-accounting and it has an internal auditor.

The Institute has a broad regional framework which comprises the Headquarters in Ibadan, two liaison offices in Abuja and Lagos and six zonal offices, representing the six geo-political zones of the country.  The regional structure of the Institute is presented as follows:

Headquarters : Ibadan
Liaison Offices : Abuja, Lagos

North-East : Bauchi
North-Central : Minna
North-West : Sokoto
South-East : Owerri
South-South : Port-Harcourt
South-West : Akure