Cone Beam Computed Tomography (CBCT) is widely used in radiation therapy for verifying treatment areas, since it provides three-dimensional image reconstruction of those tumour regions under inspection. However, organ motion is problematic during the scanning process, it causes motion artefacts on the CBCT image and can lead to mispositioning for the subsequent treatment. Moreover, patient dose is also considerable and there is a need for methods which yield acceptable image quality with as few X-ray images as possible. Although methods have been developed to handle limited projection data, such as the Algebraic Reconstruction Technique (ART); Simultaneous ART (SART); and Ordered-Subset SART (OS-SART), this study applied motion compensation to these reconstruction techniques. Root Mean Square Error (RMSE) of image is calculated to study the convergence of reconstructed images compared with the truth image. When motion was applied to a phantom and the motion compensation was used to account for the motion, the results showed that motion compensation improved the quality of CBCT image, when compared to uncompensated images. Furthermore, the experiments suggested that minimising phase error, for breathing models, was more important than minimising amplitude error.