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This paper presents a hybrid underwater navigation and control system for positioning, guidance and control of a deep-sea unmanned underwater vehicle (UUV), HEMIRE. For precise navigation of the UUV, the hybrid navigation system is designed based on strap-down IMU (inertial measurement unit) accompanying with USBL (ultra-short base line), DVL (Doppler velocity log), range sonar, depth and heading sensors. Initial localization and position reference of the UUV are performed with the USBL when the vehicles are in stationary condition. This paper also presents the characteristics of the UUV and the system constitution of the surface control unit. HEMIRE is equipped with two hydraulic manipulators, ORION, which are remotely controlled at the surface vessel via fiber optic communication. An operator can control the manipulators with a workspace-controlled master arm as well as a parallel-type master arm. This paper describes the task-oriented control of the tele-operated robotic arms mounted on HEMIRE and its application to task-oriented joint configurations.