Running of the states highly depends on accurate functioning of the critical infrastructure systems. Failure of one system can lead to massive damage or negative consequence on many others critical infrastructure systems due to their affiliation. Critical infrastructure is threatened not only by potential attacks but also accidents, natural disasters, and many other catastrophes. For these reasons, it is decidedly important to constantly improve the way of protection and preventive actions for the purpose of its protection. The present paper is focused n the critical infrastructure systems and describes innovative methods of protection of CI developed at Ernst Mach Institute – EMI and in Joint Research Centre – JRC.