The command structure of EMF reflects the non-standing character of the force.
The political-military lead of EUROMARFOR is the High Level Inter-Ministerial Committee (CIMIN), at the top level of EUROFORCES organisation, assisted by a Politico-Military Working Group (POLMIL WG) as its executive branch. The CIMIN ensures the politico-military direction of the participating nations, establishes the conditions for the employment of the force and issues directives to COMEUROMARFOR.
Under the POLMIL WG, among other working groups there is the EMF Subworking Group (EMF SG), which is composed by representatives from each one of the Nation’s Naval General Staffs. This EMF Subworking group advices the POLMIL WG on specific Naval issues and expresses the  National Naval Staff’s view on specific issues of own competence like standard operation procedures and organic matters.
The Operational Commander of the force is the COMEUROMARFOR (CEMF), who is designated every two years in a rotational basis among the National Naval Authorities (NNAs) of the 4 countries, namely:
Commandant de la Force d’Action Navale (ALFAN) for France
Comandante in Capo della Squadra Navale (CINCNAV) for Italy
Comandante Naval (COMNAV) for Portugal
Almirante de la Flota (ALFLOT) for Spain

The CEMF Operational Headquarter (OHQ) is the NNA national OHQ and his staff as CEMF relies both on his own existing National Staff and the EMF Permanent Cell (EMFPC) for the accomplishment of the duties assigned.

 The Permanent Cell is composed by a Director (a Captain) from the same country of the CEMF, 4 naval officers as National Representatives from France, Italy, Portugal and Spain, 2 naval officers as Observers from Greece and Turkey and a support secretary. 

When the Force is activated, there are three levels of command:
- High Level Interministerial Committee (CIMIN) - composed by the four EUROMARFOR Nation’s Chief of Defence and Political Director of the Ministries of Foreign Affairs;
 
- The Commander of EUROMARFOR (COMEUROMARFOR - CEMF) is at operational level.

- The Commander of EUROMARFOR Task Group (COMGRUEUROMARFOR) is at tactical level, subordinated to COMEUROMARFOR.
COMGRUEUROMARFOR is appointed, by the CIMIN, upon the activation of the Force.

  The Commanders of Euromarfor