The necessity for country clearances has been legislated through international agreements between the Republic of Italy and the United States of America.
Country clearances are based on type of travel and on what agency the traveler belongs to. If you are from another agency that is NOT DOD or attached by contract to DOD then you must file your clearance with: http://ecc.state.gov/ECC.aspx
If you are DOD then you must follow the process listed in the Italy section of the Department of Defense electronic Foreign Clearance Guide (FCG). Since the DoD FCG is directive in nature for all DoD and DoD-sponsored travel abroad, travelers regardless of component (Military, Defense Civilian, Contractor; and Defense Corporations based on the type of visit) must ensure they comply with this Guide. Details and requirements are featured and updated regularly in the electronic Foreign Clearance Guide at https://www.fcg.pentagon.mil/fcg.cfm
All country clearances must be submitted via Aircraft and Personnel Automated Clearance System (APACS) The DoD Executive Agent for the Foreign Clearance Program has authorized APACS as the web-based tool to create, submit, coordinate and approve aircraft, diplomatic and personnel travel clearances (Country, Theater and Special Area) for DoD sponsored or approved official travel. APACS will be used instead of message traffic.
APACS is also mandatory for all aircraft diplomatic clearance requests worldwide. APACS is mandatory for processing DoD sponsored personnel official foreign travel in all Combatant Commands. APACS may also be mandatory for certain types of leave travel.
The unclassified APACS web site is the preferred route for processing Country Clearances for Italy and may be found at https://apacs.dtic.mil. But, if the traveling under a protected itinerary is required then a classified APACS Country Clearance request may be submitted at https://apacs.dtic.smil.mil. Classified requests require a longer lead time for processing thorough the host nation, so please plan accordingly. Both APACS sites require the user Log onto the website and create an account, and then submit a request and have training materials, documentation, and contact to assist the traveler in properly submitting an APACS request.