The paper presents a harbour protection system developed within a national project, and studies of human systems behaviour and impact on port security architecture. The work includes practical recommendations in the following areas: (1) Networks and centralized organizations in a complex conflict environment; (2) Distribution of responsibility in a multi-level hierarchical organization (command and control dilemmas); (3) The “multi-directional” subordination problem (limits of subordination); (4) The function of the “hidden commander” in a system (is he\she ready and is she\he conscious).