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AEUF EA is established by Decree № 305 of Council of Ministers on 11.12.2008 and is set as a secondary budget spending entity to the Minister of Finance. The activity, structure, work organization and number of staff of the Agency are governed by its Rules of Procedures.
AEUF EA is managed by an executive director who represents the Agency in Bulgaria and abroad and collaborates with Bulgarian and European institutions.
The administrative management of the Agency is carried out by a secretary general, who coordinates and controls financial and economic activity and ensures a normal and efficient work environment.
The Agency is organised in general and specialized administrations. The general administration comprises of Directorate "Financial, Economic and Administrative Activities". The specialized administration is organized in four directorates as follows:
 Audits of Regional Policy Funds Directorate;
 Audits of Social Policy and Education Funds Directorate;
 Audits of Territorial Cooperation Funds and other programs Directorate;
 Legal Provision of the Audit Activity Directorate.