The modern production of weapons, military and special equipment is characterized by a high level of material and science intensity, the involvement of a large number of scientific and industrial organizations in the production process, the geographical remoteness of enterprises from each other, which requires the improvement of existing management mechanisms. External political instability as well as the ongoing change of technological structures in the economy also complicate the production activities of enterprises of the defense industry. The article analyzes the problematic issues of managing the cooperative interaction between defense industry enterprises, caused by the development of forms of inter-factory cooperation in the manufacture of weapons, military and special equipment, and also identifies guidelines that make it possible to effectively plan and coordinate the production activities of all actors involved in the implementation of the State Defense Order. As part of the study, a comparative analysis of the functionality of automated production process management systems used by defense industry enterprises has been carried out, which made it possible to identify a list of cooperation management tasks not covered by existing systems. Based on the results of the study, an automated information system for managing inter-factory cooperation has been proposed, the implementation of which will create a single information and analytical space for all participants in the manufacture of samples of weapons, military and special equipment. The article presents a conceptual scheme of this system, describes its functionality and main users. The structure of an automated management system for inter-factory cooperation is described, which consists of six modules: defense industry enterprises logistics, planning the production of samples of weapons, military and special equipment, defense industry enterprises' production capacity management, contracting management, normative reference data, the integration of the system with ERP-and PLM-systems of enterprises and departmental information systems. The article outlines the practical significance of the proposed digital management tool, describes the management tasks solved on its basis, and the expected effects of its implementation in the defense industry.