Many RGB digital cameras use a Bayer color filter array. In these cameras a full-resolution image is obtained from a mosaicked image by interpolation, and then the full resolution image is encoded. Similarly, mosaicked color filter arrays and interpolation methods for multispectral images have been proposed in recent years. The resulting full-resolution mutispectral images need to be encoded efficiently. This paper presents a new image compression method for one-shot multispectral imaging system. The proposed approach encodes the mosaicked multi-spectral image before interpolation. The decoder interpolates the image after decoding to reconstruct a full-resolution image. The simulation results show that the proposed method outperforms a conventional method, which encodes the full-resolution image after interpolation, at almost all bit rates. We also propose a heuristic color filter array design for our method that leads to lower bit rate.