The COVID-19 pandemic has caused many negative socio-economic consequences for seafarers and shipowners of such importance that, on the one hand, it inspired and, on the other hand, it became an impulse to undertake research in this direction. It seems that avoiding at least some consequences would be possible if both shipowners and ship masters operated based on safety management procedures strictly adapted to the pandemic situation. Of course, many crisis management procedures have been developed in maritime practice so far. Still, they mainly relate to such events as maritime incidents, maritime accidents, maritime disasters, oil spills, terrorist attacks, or sea piracy. However, they do not consider the specificity of a crisis situation created for the safety of the ship’s crew by the global pandemic. Its appearance made all maritime transport entities, especially shipowners, aware of the lack of preparation for such an eventuality. Based on the general recommendations of international organizations, such as the WHO (World Health Organization) or the IMO (International Maritime Organization), they began developing and implementing urgent procedures for handling ships under COVID-19 conditions. Since the recommendations were formulated generally and the pandemic spread very quickly, the prevention and response procedures for a ship found to be affected by COVID-19 were developed ad hoc and, therefore, were often flawed. Consequently, it was concluded that it is worth creating a universal model of the procedure for dealing with a sea-going ship in pandemic conditions and reducing the adverse socio-economic consequences for shipowners and seafarers. This became the primary goal of the research undertaken in this direction, and this goal was closely related to the adopted central research hypothesis. The substance of the matter comes down to the fact that knowledge of the factors causing coronavirus infections will allow the development and implementation of effective procedures for handling ships in pandemic conditions. It will also reduce the risk and consequences of coronavirus infections. COVID-19 infections can be caused by many factors that are beyond the control of the shipowner and the ship’s captain. Still, there are also those factors that they can control and thus eliminate or at least reduce the risk of contracting the coronavirus by the crew. Thus, their correct identification, ranking their importance in terms of the risk of infection, and then focusing on the elimination of the most important of them is the basis for building a universal model, in the sense of the possibility of applying to any sea-going ship in pandemic conditions. The work includes RCA (Root Cause Analysis), stratification analysis, weighted Ishikawa diagram, and Lorenz-Pareto chart. The primary sources of information used in the research came from the literature review, the analysis of normative acts, the analysis of documentation and procedures on board ships in pandemic conditions, questionnaire research, direct and focus interviews, and participant observation.