The paper aimed identification of mechanisms of non-tariff barriers used by the EU Member States that affect the intra-EU exchange of agri-food products on the example of the trade between Poland and the Czech Republic. In the beginning the paper presents, the main theoretical assumptions of the free movement of goods, based on subsequent economic integration stages according to Balassa. Next it discusses, examples of the identified actions of the Czech Republic against the agri-food products imported from Poland, together with an analysis of potential economic mechanisms resulting from these activities. The next section presents the statistical effects of trade exchange, which allows us to formulate conclusions regarding the potential consequences of the barriers. On the basis of the analysis, it was found that soft non-tariff barriers on the Czech market have not brought any significant negative effects for the overall Polish exports of agri-food products to the Czech Republic The negative consequences have been borne by individual traders, who according to the Czech authorities offered products that do not meet the requirements. Moreover, our study identified traditional non-tariff barriers introduced on the Czech market for export of all food suppliers which led to the collapse of exports from Poland, while at the same time the growth of the main suppliers from other EU Member States continued to grow.