Numerical analyses were carried out for studying on seepage problems due to seawater intrusion through the embedded rock layers of the sea-dike. A seepage analysis model, SAMTLE was developed for two-layer embankment system. The analyses by SAMTLE showed that the size of embedded rock layer had a significant effect on the seepage problems of sea-dike. If the embedded rock layer is longer and thicker, the seepage problems become more serious to water head, seepage rate and safety factor of piping in embankment. On the other hand, if the width of embedded rock layer is equivalent to the sea-dike's bottom width, the water head becomes lower and seepage rate and safety factor of piping are dramatically increasing. This makes another seepage problems such that the fresh water becomes saltier and higher seepage rates result in internal erosion of sea-dike.