Tracked vehicles are frequently used as search- and-rescue robots for exploring disaster areas. To enhance their traversability on rough terrain, some are equipped with "active flippers." However, manual control of such flippers also increases the operator's workload, particularly for tele-operation with limited camera views. To eliminate this tradeoff, we developed a shared autonomy system using an autonomous controller for flippers that is based on continuous three-dimensional terrain scanning. In our system, real-time terrain slices near the robot are obtained using three laser range sensors, and these are integrated to generate three-dimensional terrain information. In this paper, we introduce the autonomous controller for the flippers and validate the reliability of the shared autonomy system through experimental results on actual rough terrain.