Ship Drift Estimation has been widely used for weather routing navigation. Improvement of accuracy of the estimation makes energy-saving navigation more efficient. Ocean current estimation database, which is being used as ship drift speed in weather routing services, is generated by solving ocean dynamic models and by being assimilated with the satellite observation data. However, there are some differences between estimated current speed and ship drift speed which can be calculated from GPS, Log speed, Gyrocompass measurement values. This study proposes the method for ship drift estimation by means of ships' navigation data collected using AIS. In this results, the estimation error was decreased to 79% of that of ocean current estimation (JCOPE-T) in Kuroshio watershed area.