In recent years, the quality of the machined surfaces of molds for optical or medical instruments has needed improvement, and the fabrication of mirrored surfaces by means of cutting only has been gaining in importance. In order to obtain smooth surfaces, it is necessary to reduce various vibrations in the machine tool during the machining process. Many factors cause vibration in a machine tool, including feed mechanisms, pumps, and chatter. A high-speed spindle for precision machining is one source of vibration, but it is a challenge to avoid the non-repeatable run-out (NRRO) of a spindle. This study has developed an excitation system that can reduce the influence of non-repeatable run-out on machining surfaces. This paper presents a newly-developed excitation system with an excitation unit for each the X and Y direction. The excitation units consist of a voice coil motor and leaf springs, fixed on a spindle head. The tool run-out and vibration of the spindle head are measured by a displacement sensor and an acceleration sensor fixed on the spindle head, and their NRRO components are obtained through extraction using band-pass filters. By using these NRRO components as feedback signals, the excitation unit generates the force to cancel the NRRO of the tool. In order to determine the performance of the developed system, experimental evaluation was performed on a vertical 3-axis machining center. Since the spindle used for evaluation had three bearings, the measured NRRO of the tool had three peaks in the frequency domain. First, we conducted evaluation experiments under non-machining conditions, and all NRRO peaks were reduced by applying the developed system. Furthermore, there was no interference of the excitation units in the X and Y directions. Next, we evaluated the influence of the NRRO of the tool on the machining surface under finish machining conditions. The reduction in NRRO components in the measured surface profiles was observed through feedback. It was concluded that the developed system can reduce the influence of NRRO on machining surfaces.