The sustainable planned development of regional agricultural production at the current stage mostly depends on the impact of a particular mechanism aimed to provide effective functioning of the industry. The elements system of organizational and economic mechanism for management of agricultural organizations plays the main regulator role which function is of dynamic development of all fields in agribusiness. In the course of the study, the authors implemented general and specific methods of scientific knowledge, such as method of integral analysis, synthesis, comparison, grouping, induction and deduction as well as monographic method. A structure of the modern mechanism of economic management in agribusiness in which the most important role goes to the processes of digitalization and application of intelligent technologies is determined. The need to provide complex diagnostics of the economic phenomenon which will allow solving the most important problem to reduce risk factor conditions in the future is substantiated. Scientific novelty of the study is presented in the author’s approach to the diagnostics of organizational and economic mechanism functioning based on the calculations of its integral efficiency index. The direct relationship between economic policy, performed by the state structures, and constituent structural elements of economic mechanism is presented. The complex diagnostics of the considered mechanism is carried out on the example of agricultural organizations of Kurgan oblast for the period of 2000–2020. It is obtained that, in general, during analyzed period, the level of development of the agricultural mechanism in the region has not been high enough, which indicates about some difficulties in the functioning of its constituent structural elements.