In the economic system, the development trend is the use of innovative technologies of economic security. The purpose of the study is to comprehensively assess the innovative development of agricultural business in Ukraine within the framework of economic security. The leading research method has become of a modified systematic approach. The article identifies the determinants of economic security of the regions in the agrarian sector of Ukraine. The hidden properties of the influence of the competitiveness of the subjects of agrarian business on the economic security on the formation of well-being in the agricultural sector of the regions in the system of the breeding-reproduction process and their interrelation with the factors-symptoms having latent character are proved. The basis of structural transformations of the system of ensuring of economic security of the regions is developed through an integrated approach to assessing the potential financial opportunities of subjects of the agrarian sector. Complex diagnostics of the level of economic security, sustainability of the development of regions according to the components of the system have been carried out. The research results are of practical importance, since they can contribute to the development of changes in the agricultural sector of the economy.