Relevance of the research topic is determined by the expediency of strengthening food security and providing the population with safe food products. One of the important analyzed aspects was the study of non-target mutation applied methods' safety in the use of genetic engineering in the food production. The theoretical basis of the research is the scientific research results of domestic and foreign scientists in the field of food quality and safety. According to the authors, the lack of a unified information system of traceability at all stages of the food life cycle within the EAEU has a negative impact on its quality and safety. The solution to the problem will be to ensure the stability of domestic production, the availability of necessary reserves and food supplies that meet the requirements of standards. It is also advisable to apply effective technical regulation in terms of tightening the control of dual-use objects, including GMOs, by making appropriate changes to regulatory legal documents.