The system of the information protection is part of the national critical infrastructure protection. Handling of classified information is one of the critical infrastructure protection components by which individual segments of the national security system are safeguarded. In organizational terms, crisis management in cyber defense implies engaging the capacities of the relevant state bodies responsible for national security. Their activities are coordinated and guided by organizations of the executive branch and usually by the National Security Authority, as a body responsible for the coordination of the national security activities in the domain of classified information. Protection of the classified information is a crucial part of the overall critical infrastructure protection in Macedonia. The leading governmental agency for classified information protection (including information regarding terrorist activities) that plays a role of the National Security Authority in the international context is the Directorate for the Security of Classified Information. In our paper we will analyze the Macedonian experience in the protection of classified information as part of national critical infrastructure protection.