The benefits that arise from the adoption of a systems engineering approach to the design of engineered systems are well understood and documented. However, with software systems, different approaches are required given the changeability of requirements and the malleability of software. With the design of industrial cyber-physical systems, one is confronted with the challenge of designing engineered systems that have a significant software component. Furthermore, that software component must be able to seamlessly interact with both the enterprise’s business systems and industrial systems. In this paper, we present Janus, which together with the GORITE BDI agent framework, provides a methodology for the design of agent-based industrial cyber-physical systems. Central to the Janus approach is the development of a logical architecture as in traditional systems engineering and then the allocation of the logical requirements to a BDI (Belief Desire Intention) agent architecture which is derived from the physical architecture for the system. Janus has its origins in product manufacturing; in this paper, we apply it to the problem of Fault Location, Isolation and Service Restoration (FLISR) for power substations.