Projects are subject to the following controls:
- on-the-spot verification, i.e. on-the-spot visit of the projects;
- audit of the project.
 
On-the-spot verification is carried out by the implementing agency or the intermediate body who comes to inspect the project on the spot either before commencement of implementation of the project (in order to make certain whether the applicant has given the right information about itself and its activities) or during implementation of the project. The goal is to identify whether the project really exists and acts pursuant to the decision of granting support, incl. whether the declared costs have been incurred in reality, whether the costs are eligible, in compliance with legislation and certified. In addition it is observed whether the accounts of the project have been separated from the other accounts of the final recipient. It is checked whether the required procedure has been followed when organising procurement in the framework of the project or whether the requirement of asking for three tenders has been fulfilled, whether the final recipient has performed its notification obligations and whether the final recipient preserves all the original documents relating to the receipt and use of the support (incl. supporting documentation), the list of participants in the case of training (where participation is certified with a signature) and learning materials, written documentation regarding provision of the counselling service (if any), minutes of meetings, correspondence and written agreements).
 
The audit of the project is carried out by the auditors of the Financial Control Department of the Ministry of Finance, intermediate body, implementing agency or the European Commission. The audit of the project may take place at the time of implementation of the project or after termination of the activities of the project. When it comes to the project audit  the scope of inspection is similar to the scope of the on-the-spot verification.
 
In addition to the on-the-spot verification and the project audit an important source of information about implementation of the project is a monitoring report of a project. The monitoring report covers the financial and substantive progress of the project. The final recipient draws up the monitoring report by the deadlines and in the form established by the intermediate body and submits it to the implementing agency. The progress of the project is monitored on the basis of comparison of the application form/financing decision and current situation. The final beneficiary submits the final project report along with the application for final payment, specifying information about the results achieved in the framework of the project at the end of the project to the implementing agency.