The Control Service is an independent internal organisational unit of the Agency tasked with checking the facts on the basis of which payments to beneficiaries are made. To that end, it uses control systems and carries out physical checks (on-the-spot checks). The Service is also responsible for the supervision of all control systems.

On-the-spot checks are performed before, during and after the implementation of agricultural policy measures in accordance with Slovenian and European regulations. The Service also carries out ex-post checks on the work of controllers and other institutions responsible for performing on-the-spot checks.