The developing global information society has posed new economic and legal problems due to the increase in the use of the Internet and the development of innovations in the digital economy. The security of innovations in information systems has recently become the main problem in the development of informatization processes in the transport industry. Topical aspects are threats of information leakage and viruses. Automated information systems have opened up new opportunities for organizing interregional information economic activities, but at the same time they have become one of the most vulnerable parties, attracting intruders both from among the company’s personnel and those working outside the enterprise. The most important security problems of regional innovation clusters include the problems of virus penetration, information theft, the decrease in the efficiency of computers due to the use of their resources by attackers for other purposes, the high speed of threat modification, and the imperfection of the legislative framework. Distributed systems and systems with remote access have brought to the fore the issues of protecting processed and transmitted information. For specific regional innovation clusters of the transport industry, the security policy should be individual. It depends on the specific information processing technology, software and hardware, databases and other elements used.