The management structure of the programme consists of the following institutions:
Joint Secretariat (JS) is the most important contact point for project applicants. It provides daily assistance to applicants and project managers during preparation of project ideas and implementation of projects. The JS is responsible for the daily implementation and monitoring of the programme, assists the Managing Authority and Monitoring Committee, and, where appropriate, the Audit Authority and the Group of Auditors in carrying out the respective duties. The JS is hosted by Enterprice Estonia and located in Tartu. The JS is supported by the Information and consultation point in Riga and located at the State Regional Development Agency.
Monitoring Committee (MC) is composed of maximum seven members from both Estonia and Latvia. Members of the MC include representatives of national, regional or local level authorities and socio-economic partners. The MC is responsible for selecting operations, monitoring project implementation, making changes in the Programme Manual, and proposing amendments to the Cooperation Programme.
Managing Authority (MA) is responsible for efficiency and correctness of management and implementation of the Programme. The tasks of MA are carried out by the Estonian Ministry of Finance, Cross-Border Programme's Implementation Unit, which signs subsidy contracts, verifies that the co-financed products and services are delivered and that the expenditure declared by the projects has actually been incurred and complies with Community and national rules. The MA draws up and submits payment applications for the ERDF funds to the European Commission, receives payments and pays out subsidies to the projects. The MA also fulfils certifying functions, thus it is responsible for the accuracy of expenditure statements and compliance of the eligible expenditures with Community and national rules.
Financial Control (FC) system in Estonia and Latvia is set up by the member states. FC bodies are responsible for verifying that the co-financed products and services have been delivered, expenditure declared by the beneficiaries has been paid and that it complies with applicable law, the operational programme and the conditions for support of the project. Partner reports are verified according to national conditions and proceedures that are described in the Programme Manual and national FC reporting guidelines.
National Responsible Authorities (NRA) of the programme are the Estonian Ministry of Finance and the Latvian Ministry of Environmental Protection and Regional Development. These institutions are responsible for implementation of the programme in their countries. National responsible authorities establish coordination mechanisms between European territorial cooperation programmes and structural funds' programmes in Estona and Latvia.
Audit Authority (AA) is situated at the Financial Control Department of the Estonian Ministry of Finance, in Audit Unit III. The AA ensures that audits are carried out to verify the effective functioning of the management and control system of the programme, and correctness of the controls carried out on the projects.
Group of Auditors (GoA) has a task to assist the Audit Authority. GoA comprises of the representatives of the AA and of the Internal Audit Department of the Latvian Ministry of Environmental Protection and Regional Development.