The paper discusses importance of security environment establishment process, as well as its particular stages, including security-oriented analysis and assessment of safety critical instrumentation and control systems (I&Cs). One of the underlying ideas behind the assessment approach is in performance of gap analysis, considering influence of human, technique and tool, and application of Intrusion Modes and Effect Criticality Analysis (IMECA) technique. It allows application the approach to various safety-critical systems, including Field-Programmable Gate Arrays (FPGA)-based instrumentation and control systems (I&Cs). In order to establish secure development and operational environment for I&Cs, the requirements of the international standards to Nuclear Power Plants I&Cs security are analyzed and the proposed technique is illustrated using security case for FPGA platform RadICS.