Currently, active work is underway to introduce a project-based approach to the management of new product production processes. However, even if the need to implement project management is undeniable, the question arises of the pitfalls in implementing these innovations into the defense enterprises. Based on this, this work aims to determine organizational problems of implementing project management system into an enterprise of the defense industry. The following methods were used to collect data: in-depth interviews with employees of the company, taking a direct and key part in the PM processes; study of internal regulatory and other documentation on the research object; conducting a survey of employees. The research revealed the use of project management tools that are developed mostly in procurement management. The main problems of project management implementation are in scheduling, communications and integration management. The weaknesses in terms of the support provided for the implementation of projects by the enterprise include such areas as the availability of standard project management software and the organization of permanent trainings on project management. Based on the problems revealed, some recommendations are made for implementation of project management system in the enterprise of the defense industry.