Recently, the solution of complex problems of automation of organizational learning systems and the improvement of its individual areas has not always been sufficiently developed. This negatively affects the systematic approach to this problem in the process of training cadets of the institute, and often leads to unreasonably and unjustifiably large expenditures of finances and resources. All the presented problems and factors, in modern conditions, predetermine the special significance of the development of the process of automating the system for organizing the training of a military institute. The formation of a strategic conception for automating the system for training organization of cadets at the Naval Institute implies an increase in the efficiency of the educational process. The article defines ways to solve this issue on the basis of a systematic approach and the use of system diagnostics of automated training systems and training facilities at specific departments of the institute, based on modern weapons, information technologies, special information databases. And also, on the basis of expert assessments, software and technical methods for automating organizational training systems at the departments of the Naval Institute were determined. An opinion was expressed on the solution of interdepartmental disagreements and the creation of an engineering center that unites scientific personnel for the mass production of automated workstations and a software product for computer (complex) simulators of departments.