The EFCA coordinates activities on land and in Community and international waters, as appropriate. This is done through the joint deployment plans, the vehicle through which the EFCA organises the deployment of national human and material means of control and inspection pooled by Member States. The deployment of pooled national means is coordinated by the EFCA through coordination centres in charge in a Member State or the presence of national coordinators is at EFCA premises.

While Member States are responsible for applying the rules on their own territory, in waters under their sovereignty and jurisdiction and on fishing vessels flying their flag, wheresoever their activity is carried out, the Agency has been designed to act as a facilitator enhancing cooperation and ensuring that legislation is implemented in a systematic, uniform and effective way. Pooling national efforts at European level should overcome shortcomings which may arise because of the different resources and priorities authorities allocate to their own controls and inspections.

In Community waters, two criteria have to be met before the JDPs can be established. The fish stocks concerned must be subject to a long-term recovery plan or a multi-annual management plan. In addition, a specific control and enforcement plan, adopted by the Commission, must be in place. In international waters, the Commission has entrusted the Agency with the inspection activities, trough carrying out JDPs both at sea and at landing, which are delivering the international obligations of the EU.