The paper presents, the main types of hazards for personnel, equipment and electric power systems which should be taken into consideration in the design of computer-based systems applied in electric power industry, as well as threats to the systems from security point of view. Additionally, examples of problems are described which appeared in carrying out, for the first time in Polish electric power sector, the safety analysis of a extra-high voltage substation software interlockings. The problems were mainly connected with the lack of standards or guidelines on the design of computer-based systems applied in power substations and the lack of exact data on failures of substation components, breakdowns and accidents at substations and large failures of the national electric power system. The data which are used for the traditional relay-based control systems design are insufficient. In conclusion some suggestions are given to improve the situation.