With the deterioration of the technical ability of crew members of mixed nationalities, the frequency of incidence of marine accidents such as collisions, running agrounds or ship fires; also tends to increase gradually. The development of a methodology for the reliability analysis of the means available for the prevention of marine accidents originating from human errors is becoming highly desirable in recent years. This paper presents an analytical method for the estimation of the incidence probability of accidents during the functional design applications of marine systems. This process of probability estimation is divided into three stages. Firstly, the qualitative analysis of the reliability of the functional system under design is carried out using the fault tree. Next, the probability of human error and the frequency of device failure in the functional system are decided by using a degree of unsafeness; which is defined as similar to the sense scale based on the experience and ingenuity of engineers. Lastly, the improved choice of items are used in the calculation using the Boolian function to reduce the risk of accident probability in the functional system. The effects of countermeasures adopted are predicted quantitatively in the calculation based on the fault tree analysis and the fuzzy theory. As a practical example, the conditions for reducing the incidence of fire spreads during a ship fire are investigated using the proposed method.