An analysis of the problem of adapting supply chains in a modern environment shows the need for a change in the use of the principles of security and fault tolerance of systems, the transformation of models and supply chain management systems (SCM) towards a balance between reliability and flexibility, between efficiency and complexity. The purpose of the article is to formulate new principles and methods of proactive management of an organization according to the criterion of «acceptable risk» at all stages of the life cycle as a whole. The article explores new methods for the formation of an integrated SCM methodology, as a complex organizational and technical system (COTS), based on enterprise engineering, an integrated architectural approach, risk forecasting and proactive management in a high uncertainty environment. The scope of risk management and forecasting should be extended to the entire integrated supply chain (ISC), including the operation of facilities. The principles and new practices of supply chain fault tolerance have been formed based on the interaction of standard architectures with the organization's processes, a program for ensuring business continuity, which reduces the level of threats and losses.