The responsibility for the programme has been transferred in 2005 from the External Relations to the Enlargement Directorate General. It has a dual management system as the part of the programme covering Serbia, Montenegro and Macedonia is operated by the Thessaloniki based European Agency for Reconstruction (EAR) while the rest of support follows a deconcentrated system as it is managed by the Commission's delegations to Croatia, Bosnia and Herzegovina and Albania.
In 2005, the programme's management was shifted from the External Relations department to the Enlargement Directorate General. It employs a dual management structure: the part focused on Serbia, Montenegro, and Macedonia is overseen by the European Agency for Reconstruction (EAR) in Thessaloniki, while the rest of the support is managed through decentralized structures under Commission delegations in Croatia, Bosnia and Herzegovina, and Albania.