Studies on the ship's automatic navigation & berthing control have been continued by way of solving the ship's mathematical model, but the results of such studies have not reached to our satisfactory level due to its non-linear characteristics at low speed. In this paper, the authors propose a new control system which can evaluate as closely as captain's decision-making by using the FNN(Fuzzy Neural Network) controller which can simulate captain's knowledge. This controller contains the concept of safety according to channel width. The learning data are drawn from ship Handling simulator(NavSim NMS-90 MK III) and represent the ship motion characteristics internally. According to learning procedure, the FNN controller can tune membership functions and identify fuzzy control rules automatically. The verified results show that the FNN controller is effective to incorporate captain's knowledge and experience of manoeuvrability in channel.