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The paper is devoted to the safety of complex technical systems of systems (SoS) through the improvement of engineering processes at all system lifecycle stages. The safety of complex technical facilities (such as nuclear and conventional power plants, offshore oil and gas platforms and chemical processing plants) is analyzed based on the systems theory and SoS engineering. The safety concept discussed is the development and implementation of engineering process constraints to identify and prevent engineering inconsistencies which endanger systems safety. The method proposed consists of inconsistency classification as well as practical recommendations on how to formulate and implement safety constraints. The paper is based on the project implementation experience of IBS in 2010-2012 in the capital industry in Russia.