The article is dedicated to an analysis of the control system of one of the instruments used by the state during the implementation of the programmes co-financed from the EU financial instruments. Their basic advantage is that they generate a lower risk of swindling as beneficiaries have to return the funds they have received. Beneficiaries have to provide repayment security for such instruments, e.g. bills of exchange or collaterals, and in the case of non-repayment beneficiaries can be subject to standard debt recovery proceedings. At the same time, these instruments are less advantageous to the beneficiaries than, e.g. non-returnable subsidies, since they need to return the funds invested. However, overregulation related to this kind of support and the need to return them may make beneficiaries reluctant to use them. That is why the specifics of financial instruments should be take into account when the frequency and scope of beneficiaries’ audits are set.