With the aim of independence in the country's strategic issues, it is necessary to facilitate the presence of knowledge-based companies in the country's economic system. However, in military matters, especially missile plans, there are certain limitations. This research was conducted in an analytical-descriptive way and aims to investigate the administrative challenges of the presence of knowledge-based companies in the aforementioned projects. The main contractor of missile designs is the Ministry of Defense, which ultimately delivers the products to the armed forces. However, this authority is fully delegated to the IRGC and the conflict between the internal regulations of this organization and the administrative regulations of the executive branch regarding the issuance of licenses for the activities of knowledge-based companies, in the area of licensing, security inquiries, support methods, model statutes, and the granting of intellectual property documents, causes limitations. Strict enforcement has been done on the mentioned companies, and in the end, a smaller number of active companies in this field are able to achieve their scientific goals. It is suggested that the government is responsible for following up on the matter from the Supreme Leader and in coordination with the Revolutionary Guards and then the plan in the meeting of the heads of the three powers, a specific by-law regarding the activity of knowledge-based companies in the missile field has been developed, which includes the flow of inquiries, inspections, licensing, ownership documents and The way to support them should be clearly defined a