A towed vehicle “Flying Fish” has been developed for ocean observations. The motion of the long towing cable used in the observations is essential for the towing system, so that an accurate mathematical model of the towing cable must be determined. A design for a motion controller using a mathematical model of the cable motion based on mode expansion was developed for the system. This provides an accurate mathematical model of the cable motion which has fewer parameters than other methods, and this enables us to apply an advanced control system. Furthermore, unsteady effect of lift of the wings on stability of the control system was discussed. The designed motion controller was tested in field experiments and its efficiency was confirmed.