Matsyafed  is an Apex Federation of 651 primary level Fishermen Development Welfare Cooperative Societies. Of the 653 primary societies 335 are in the marine sector, 198 in the inland sector and 118 are women co-operatives. The total membership in these societies is more than 3 Lakh. The paid-up share capital of the Federation is ₹150 Crore. The primary societies are clubbed into 51 clusters for administrative convenience based on geographical area.

The administration and management of Matsyafed is normally vested with a 22 member Board of Directors voted to power through a democratic system of election from members of the affiliated primary co-operatives.  The Chief Executive is the Managing Director. There are 7 Divisions to carry out all the activities of the organisation. Each division is headed by Deputy General Manager (for Personnel Division – Personnel Manager). Planning, Project Formulation, Implementation, Monitoring, Reviewing and Evaluations in thier areas of operation are carried out at the Division level.

Matsyafed has 10 District Offices one in each of the nine Maritime districts and one in the Inland district of Kottayam. The District Managers with a team of supporting staff co-ordinate and supervise all the activities at the district level. In every district there are 3 – 7 Project Offices (Field Level Cluster Office) and the Project Officer is in charge of this office. The Project Officer functions as a friend, philosopher and guide to the fishermen community and co-ordinates the implementations of the various projects at the grass root level.