The berthing maneuver requires high maneuvering techniques because the navigators have to stop the ship at a specified point with decreased maneuverability in restricted water area. Therefore, the automation of berthing maneuver has been gaining increased attention from the marine transportation industry. To construct a reliable automatic berthing system, it is desirable to apply a flexible method in regards to changing the ship's maneuverability, similar to the human's manual berthing maneuvering procedure. In this study, an automatic berthing maneuvering method was developed that does not require gain adjustments based on the experience of specialists or model tests, and is flexible for maneuverability changes of the ship as in manual berthing maneuvering procedure. This was accomplished by introducing an optimal control with variable gain based on the statistical model for maneuvering the ship, which was identified in real-time using actual navigation data. From the results of the experiment, it was confirmed that the method developed in this study was effective.