Safety and efficiency of fishing fleet activity depend largely on the quality of management decisions. Cause-and-effect relationships of accidents involving fishing vessels were identified by means of an analysis of emergencies and fishing incidents. The suggested method of risks calculation is based on the use of statistical methods, fuzzy sets/expert estimations method and the probability theory. The following most common tasks are presented and solved: - there is an impact of two or more independent negative factors/events on the vessel such as failure of a sonar, a vessel operator error, another vessel operator error. - a transport vessel carries out loading and unloading of fishing vessels under different environmental conditions. The value of the risk of an emergency incident is determined. - the fishing vessel navigation performs under various meteorological conditions. A priori probability of incident-free operation is calculated according to expert estimations.