For tracked vehicles moving over rough terrain, it is important to avoid rollovers and rapid motion. To realize smooth locomotion on rough terrain, some tracked vehicles are equipped with "active flippers." Such flippers increase the traversability and stability of tracked vehicles. However, their control increases the operator workload, especially in the case of teleoperation. To eliminate this problem, we have developed an autonomous controller for generating terrain-reflective motions of flippers. Terrain information is obtained using laser range sensors that are located at both sides of our tracked vehicle testbed. Using this system, operators only have to specify a direction to the robot, following which the robot traverses rough terrain using autonomous flipper motions. In this paper, we introduce a strategy and an algorithm for the controller for active flippers and validate the reliability of the system through experimental results on rough terrain.