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The spatiotemporal spectra of a video that contains a moving object form a plane in the 3D frequency domain. This plane, which is described as the theoretical motion plane, reflects the velocity of the moving objects, which is calculated from the slope. However, if the resolution of the frequency analysis method is not high enough to obtain actual spectra from the object signal, the spatiotemporal spectra disperse away from the theoretical motion plane. In this paper, we propose a high-resolution frequency analysis method, described as 3D nonharmonic analysis (NHA), which is only weakly influenced by the analysis window. In addition, we estimate the motion vectors of objects in a video using the plane-clustering method, in conjunction with the least-squares method, for 3D NHA spatiotemporal spectra. We experimentally verify the accuracy of the 3D NHA and its usefulness for a sequence containing complex motions, such as cross-over motion, through comparison with 3D fast Fourier transform. The experimental results show that increasing the frequency resolution contributes to high-accuracy estimation of a motion plane.