Subpixel mapping (SPM) is a technique for predicting the spatial distribution of land cover classes in remote sensing images at a finer spatial resolution level than those of the input images. Indicator cokriging (ICK) has been found to be an effective and efficient SPM method. The accuracy of this model, however, is limited by insufficient constraints. In this paper, the accuracy of the ICK-based SPM model is enhanced by using additional information gained from multiple shifted images (MSIs). First, each shifted image is utilized to compute the conditional probability of class occurrence at any fine spatial resolution pixel (i.e., subpixel) using ICK, and a set of conditional probability maps for all classes are generated for each image. The multiple ICK-derived conditional probability maps are then integrated, according to the estimated subpixel shifts of MSI. Lastly, class allocation at the subpixel scale is implemented to produce SPM results. The proposed algorithm was tested on two synthetic coarse spatial resolution remote sensing images and a set of real Moderate Resolution Imaging Spectroradiometer (MODIS) data. It was evaluated both visually and quantitatively. The experimental results showed that more accurate SPM results can be generated with MSI than with a single observed coarse image in conventional ICK-based SPM. In addition, the accuracy of the proposed method is higher than that of the existing Hopfield neural network (HNN)-based SPM and the HNN with MSI.