The Agency's mission is to promote the highest common standards for control, inspection and surveillance under the Common Fisheries Policy.

The EFCA will function at the highest level of excellence and transparency with a view to developing the necessary confidence and cooperation of all parties involved and, in so doing, to ensure effectiveness and efficiency of its operations.

European Union governments agreed to establish the Agency in the 2002 reform as part of the drive to instil a culture of compliance within the fisheries sector across Europe. In April 2005, they adopted the necessary legislation with the Council Regulation 768/2005. Its primary role is to organise coordination and cooperation between national control and inspection activities so that the rules of the Common Fisheries Policy are respected and applied effectively.