March 11th, 2011, the 9. 0M earthquake induced Tsunami attacked the northeast coast area in Japan. A great amount of breakwaters have been damaged seriously in this disaster, including the world deepest breakwater-Kamaishi breakwater. According to a GPS (Global Positioning System) wave height record, long time duration of high hydraulic head difference between the seaside and harbor side of breakwater was observed in Kamaishi bay. It can be presumed that the instability of caisson type composite breakwater was attributed to the seepage flow which was generated by gradually raised hydraulic head difference in the rubble mound underneath caisson from sea side towards harbor side. This phenomenon is different from the wind wave induced instability problem on caisson type composite breakwaters. By this motivation, in order to find out the instability mechanism of caisson type composite breakwaters against Tsunami, both theoretical analysis and laboratory experiment have been represented in this paper. By illustrating flownets and calculating seepage force inside the rubble mound, a definition on factor of safety-a new parameter "a" is embedded. Parameter studies were carried out to discuss the relationship between the hydraulic head difference and the factor of safety. A scale of 1/100 model was established in laboratory. Pore water pressure inside rubble mound under steady flow and several hydraulic head differences were observed and piping phenomenon was reproduced. By comparing the results of laboratory experiment and theoretical method, It was found that the parameter " a " reflects the development of seepage force affecting on stability of rubble mound, and it indicates the unstable area along the rubble mound crest. This method can be applied for preventing the rubble mound failure under Tsunami conditions. It can be said that it is necessary to take the seepage flow into account when making a design of the caisson type composite breakwater against Tsunami.