The BOBP-IGO is a tri-layered organisation headed by the Governing Council drawn from the constituent Ministry/Department of Fisheries of the Four Member-Countries.

The Governing Council is the apex body of the Organisation and functions through the BOBP-IGO Secretariat located in Chennai, India. The Secretariat is headed by the Director, appointed by the Governing Council, and Professional and Administrative Staff.

To help the Governing Council and the Secretariat in designing the work plan and undertake performance evaluation, the Governing Council appoints the Technical Advisory Committee (TAC) of the BOBP-IGO. The TAC comprises of leading Marine Fisheries Research Institutes/Organisations of the respective Member-Countries.

The TAC meets once in a year to draw up and evaluate the work plan and submits its recommendations to the Governing Council for review and approval.