The interest for the registration between 2D ultrasound (US) and preoperative CT or MR images has been growing for US-guided diagnosis, intervention, and surgery. In our previous study, we proposed a real-time and automatic registration system between two images of the liver without any help of positioning sensors. We have confirmed that the system can provide an accurate and reliable registration performance, if sufficient features are included in a current US image. In this paper, we propose a robust position estimation system of a moving liver lesion based on the previously proposed registration system. The system indirectly but reliably estimates the lesion position by registering a US image including sufficient features to 4D MR images, even if the US image does not include the target lesion. The proposed system is evaluated on three clinical datasets, through both qualitative and quantitative evaluations. Experimental results show that the registration error for target lesions is less than 5 mm on average, which is considered acceptable for many clinical applications.