The article shows the difficulties and risks that arise when implementing the HACCP system in Russian enterprises of the food industry. An expert group of specialists of different profiles and competencies identified the risks using the brainstorming method. An analysis of the risks that arise during the development and implementation of a food safety system based on the principles of HACCP showed that according to the source of occurrence, they are divided into two groups: external and internal. External risks include the risks posed by the state, which, according to experts, are the most significant. These include: poor educational work; lack of explanatory materials on the preparation and implementation of the system; lack of harmonization of HACCP requirements with the regulatory framework of the Russian Federation; complex terminology, complex presentation of information, etc. Internal risks include risks from the management and personnel of catering enterprises: a formal approach to the creation and implementation of the system, a low level of education for linear personnel, an imperfect incentive system, non-compliance with discipline in maintaining records and documents of the system, etc. The article describes actions to minimize the identified types of risks.