A towed vehicle "Flying Fish" has been developed for ocean observations. The motion of the long towing cable used in the observations is the dominant motion of 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 a finite number of eigenfunctions of the cable motion equation is developed for the vehicle. Results of numerical simulation were compared with results from a lumped mass method and it was shown that the transient characteristic of the cable motion depends on the method used for the mathematical model. The designed motion controller was tested in field experiments and its efficiency was confirmed.