The Monitoring Committee (MC) is the main decision body of the Programme. The MC is responsible for monitoring the Programme’s implementation and reviewing the Programme’s overall effectiveness towards meeting its objectives. Both partner countries are equally represented in the JMC.

The Steering Committee (SC) is set up by the MC and acts under its responsibility for the selection of operations. The SC reports to the MC.

The Managing Authority (MA) of the Programme is the Special Service Managing the "European Territorial Cooperation" Objective Operational Programmes. It is assisted by the Joint Secretariat and is responsible for managing and implementing the Programme in accordance with the principle of sound financial management. The MA ensures that the different Programme bodies interact in a smooth way.
The Joint Secretariat (JS) is set up under the legal responsibility of the Managing Authority. The two bodies work closely together. Under the MA’s supervision, the Joint Secretariat assists the JMC, the Managing Authority and, where appropriate, the Audit Authority in carrying out their respective functions.
Antenna of the Joint Secretariat
An antenna of the Secretariat is established in the Republic of North Macedonia. The role of the Antenna is focused at the national level. In particular, it supports the Programme’s communication strategy and the Programme’s potential beneficiaries and project partners in their activities.

The designated Certifying Authority (CA) of the Programme is the Special Service "Certifying and Verifications Authority of Co-funded Programmes" - Units, A, B and C of the Greek Ministry of Economy and Development . The Certifying Authority is responsible for certifying statements of expenditure and applications for payment before being sent to the Commission. The Certifying Authority is independent from the Managing Authority and the Audit Authority.

The Audit Authority (AA) of this Programme is the Financial Αudit Committee (EDEL), at the Ministry of Finance, General Accounting Office in Greece. The Audit Authority is responsible for verifying the effective functioning of the management and control system of the Programme and on an appropriate sample of projects and relevant sampling methodology.
The  National IPA Coordinator (NIPAC) is the main counterpart of the Commission for the overall process of: strategic planning, coordination of programming, monitoring of implementation, evaluation and reporting of IPA II assistance. In particular, the NIPAC shall coordinate with the administration in the Republic of North Macedonia and ensure that the administration takes all necessary steps to facilitate the implementation of the Programme. The designated NIPAC is the Ministry of European Integration in the Republic of  North Macedonia.

The Operating Structure (OS) shall coordinate the participation of project partners from the former Yugoslav Republic of Macedonia and other IPA II beneficiaries in the Programme. The designated Operating Structure is the Ministry of Local Self Government in the Republic of North Macedonia.

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