The institution is administered by the Governing Council.The Secretarial Office is headed by the Executive Director of the Institution with necessary infrastructure under his charge. This Secretarial office is in Rail Bhawan in New Delhi.

The activities of Institution are spread over Indian Railways. There are 16 centres with their jurisdiction over the respective Zonal Railways. In addition, there are also Centres at the RDSO, Lucknow and Indian Railway Institute of Civil Engineering, Pune with Jurisdiction over these respective organisations. Each zonal centre is subdivided into sub-centres, located at the Divisional Headquarters of all the Zonal Railways. The  Principal Chief Engineer of each Zonal Railway is Ex Officio Chairman of the Zonal Centre.

The Chief Administrative Officer (Construction) of each zonal railway is the Ex-Officio Co-Chairman of the zonal centre.