Disclosed are systems and methods for protection of a technological system (TS) from cyber attacks. An exemplary method comprises: obtaining a real state of the TS; initializing a cybernetic control system (CCS) by synchronizing the CCS with the TS; comparing, by the CCS, the real state of the TS with an ideal state of the TS; based on the comparison, identifying a deviation of the real state of the TS from the ideal state of the TS; when the deviation is identified, checking an integrity of at least functional interconnections of the states of one or more elements of the TS; determining whether the ideal state of the TS is a modeling error based on one or more confirmed sustained functional interconnections between elements of the TS; and identifying anomalies in the TS based on one or more disturbed functional interconnections between elements of the TS.