Structure of the system of implementation of structural funds through 2007-2013
The Ministry of Finance is the managing authority, paying authority and auditing authority of the operational programmes.

The Foreign Financing Department of the Ministry of Finance performs the role of the managing authority. The main duty of the managing authority is to ensure implementation of the structural funds in compliance with legislation and purposes. The managing authority is thus responsible before the European Commission for implementation of the structural funds on the whole and also performs the role of the European Commission as the main partner in the implementation phase.

The EU Payments Department of the Ministry of Finance performs the duties of the paying authority. The main duty of the paying authority is to certify to the European Commission the eligibility of the expenditure and to apply for structural support.
The auditing authority is the Financial Control Department of the Ministry of Finance. The auditing authority is an external auditor with regard to the system of application of structural funds, who carries out independent audits regarding the application system as well as supported projects.

The leading ministries of the operation programme coordinate preparation of the operational programmes, call and lead the operational programme's monitoring committee and bear liability for preparation of the communications plan of the operational programme and submission thereof to the European Commission.

The intermediate bodies prepare the terms and conditions of granting and using support with regard to the measures in their area of government and are thus responsible for attainment of the substantive goals defined in the operational programmes within their area of government.

The implementing agencies process support applications, check payment applications and eligibility of expenditure, make payments, exercise supervision over projects and counsel final recipients.