This article is a continuation of the authors’ study on the ways to ensure safety in the Air Traffic Management (ATM) system. It directly refers to the processes of risk management involving, in particular, risk management in (air) transport. The mai aim of this paper is to present and indicate the hazard identification and risk assessment tools that can be used in air transport and to apply one of them for a risk analysis of a specific ATM originating case. This is why, after a short introduction, describing the background of the research as well as literature review, the risk management process as such is characterized. It is shown in a schematic way and its main components are identified. At the same time, from the entire management process, the risk assessment procedure is highlighted as its most crucial part. Then, general hazards identification techniques, risk analysis and assessment tools are described, with an indication that they can also be implemented in air transport, if compatible with ICAO Standards and Recommended Practices (SARPs). In the following part, the process of risk assessment in air transport, based on the Safety Management Manual, using a safety risk tolerability matrix, is characterized. Finally, in this article, an exemplary risk analysis is carried out, focusing on a selected case arising from the ATM field. For the analysed case, safety risk hazards and their possible effects are identified and then assigned to the Intolerable, Tolerable and Acceptable regions. The entire paper is summarized and conclusions are drawn in relation to the publication’s main goal. Attention is also paid to the potential causes of appearance of hazards including, first of all, lack of adequate verification procedures, as well as people’s competence and last but not the least human errors, being the reason for 70-80% of unwanted transport accidents.