Food production is one of the key sectors of the food industry in the Czech Republic and the European Union. Its direct link to the primary agricultural sector is also crucial, from which it takes inputs, which it further processes and markets. A necessary condition for this process is the quality and safety of the commodity produced. The businesses must demonstrate food quality and safety through an effective system of traceability and traceability of these criteria. These conditions significantly affect aspects of production and logistics. The paper is focused on the dairy industry. This industry forms an essential part of the entire agri-food chain. Processes in enterprises of this type are specified in that several regulations affect production and logistics operations. Raw materials and products are perishable. On the other hand, the customer expects a quality and safe product at the right time. The paper's main aim was the identification of risks in individual phases of the dairy industry logistics processes. The area of purchasing, production, and the transport was examined in particular. The secondary aim was to expand theoretical knowledge of dairy management. Expert studies and scientific articles in this area are insufficient.