The article examines the formation of cyber-physical systems in Azerbaijan and some topical problems of their complex security. Moreover, the article highlights the features and problems of digital transformation of state institutions effected by cyber-physical systems. It classifies the main pillars of cyber-physical systems (algorithmic security, resistance to denials, power supply security, artificial intelligence security, functional reliability, structural reliability, adaptability, human factor). The need to improve the network and communication infrastructure is justified. The ways to develop the field of Soft Engineering for the regular operation of cyber-physical systems at the national level, to solve some issues related to chip supply, protection of personal data, existing legal problems, and certain personnel are shown. Correspondingly, the main research trends in the field of cyber-physical systems are identified.