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Recent progress in magnetic resonance electrical impedance tomography (MREIT) research via simulation and biological tissue phantom studies have shown that conductivity images with higher spatial resolution and accuracy are achievable. In order to apply MREIT to human subjects, one of the important remaining problems to be solved is to reduce the amount of the injection current such that it meets the electrical safety regulations. However, by limiting the amount of the injection current according to the safety regulations, the measured MR data such as the z-component of magnetic flux density Bz in MREIT tend to have low SNR and get usually degraded in their accuracy due to the nonideal data acquisition system of an MR scanner. Furthermore, numerical differentiations of the measured Bz required by the conductivity image reconstruction algorithms tend to further deteriorate the quality and accuracy of the reconstructed conductivity images. In this paper, we propose a denoising technique that incorporates a harmonic decomposition. The harmonic decomposition is especially suitable for MREIT due to the physical characteristics of Bz. It effectively removes systematic and random noises, while preserving important key features in the MR measurements, so that improved conductivity images can be obtained. The simulation and experimental results demonstrate that the proposed denoising technique is effective for MREIT, producing significantly improved quality of conductivity images. The denoising technique will be a valuable tool in MREIT to reduce the amount of the injection current when it is combined with an improved MREIT pulse sequence.