In this paper we propose the scheme of diagnosing the problem situation of complex system development based on the analysis of structural properties of a cognitive-map-based model of the system development. It allows exploring different types of problem situations related to the interaction of active agents, the adverse effect of the environment and the structural features of the system. The distinctive feature of the proposed scheme is that the problem situation is considered in the whole. This is aimed to determine priorities for problem solving, depending on their causes.