The new unit was designated the Mine Counter Measures Force Mediterranean (MCMFM) and was subordinate to the Com NAVSOUTH.

As result of this reorganization four Mediterranean maritime commands (COMEDCENT, COMEDEAST, COMEDNOREAST, COMGIBMED) were stood down, and COMSUBMED and COMMARAIRMED were transformed in special entities of NAVSOUTH, as COMSUBSOUTH and COMMARAIRNAPLES.

[2] Israel signed an Exchange of Letters (EOL) on 4 October 2006, regarding Operation Active Endeavour, followed on 6 June 2007 by a Tactical Memorandum of Understanding (TMOU) between CC-Mar Naples and the Israeli Navy.

[4] The mission of COM MC Naples was to "plan, conduct and support the full range of military operations anywhere in the world in order to deter aggression, contribute to effective crisis management and promote peace, security and stability.

To enforce this embargo, NATO started Operation Unified Protector which included both air and maritime elements.

Operation Unified Protector officially ended on 31 October 2011, after the Libyan rebels had formed a transitional government.

It was commanded by an Italian three-star Admiral with staff coming from 17 countries including Albania, Bulgaria, Canada, France, Germany, Greece, Italy, the Netherlands, Norway, Poland, Portugal, Romania, Slovenia, Spain, Turkey, the United Kingdom and the United States.