Nonstationary optimal regulator (NOR) is one of the effective methods for positioning control of vibration systems. NOR corresponds to an LQ regulator utilizing time-varying weighting functions and produces positioning trajectories taking the vibration characteristic of a controlled object into account. Generally, many positioning or tracking mechanisms such as information equipments, machine tools and robots adopt dual-stage actuator systems (DSASs). DSASs consist of coarse and fine actuators and realize efficient and high performance responses. However, the control method for DSASs with mechanical flexibility has not been fully addressed. This study utilizes the NOR technique for positioning control of DSASs taking spring and damping elements of controlled objects into account. We use a proper combination of time-varying weights for this problem. The effectiveness of this method is verified by numerical calculations and experiments.