An optical information authentication system using binary holography is proposed recently, with high security, flexibility and reduced cipher-text size. Despite the success, we point out one limitation of this system that it cannot well verify scaled and rotated versions of correct images and simply regard them as wrong images. In fact, this limitation generally exists in many other optical authentication systems. In this paper, a preprocessing method based Fourier transform and log polar transform is employed to allow the optical authentication systems shift, rotation and scale invariant. Numerical simulation results demonstrate that our proposed scheme significantly outperforms the existing method.