The 2011 off the Pacific Coast of Tohoku Earthquake on the 11th of March, 2011 had induced a gigantic Tsunami and caused the catastrophic damage in the northeast coast area of Japan. Lots of breakwaters have been seriously damaged in this disaster, including the world deepest breakwaters, Kamaishi Harbor Mouth Breakwaters. According to a wave height recorder, a large hydraulic head difference between the seaside and harbor side of breakwaters was observed for long duration of several minutes or more. Such a hydraulic head difference as observed generates the seepage flow in the rubble mound underneath the caisson. The seepage flow is considered one of the influential factors causing the instability of caisson type composite breakwaters. In order to find out the instability mechanism of caisson type composite breakwaters against tsunami, 1) the pop-out phenomena of armored blocks on the mound, 2) the possibility of shear failure of rubble mound and 3) the reduction of bearing capacity of rubble mound due to seepage flow are investigated. Both theoretical analysis and laboratory experiment are represented in this paper. The safety factors for the pop-out failure and shear failure of rubble mound were theoretically derived. A scale of 1/100 model experiment was performed in laboratory. Loading tests were carried out to investigate the reduction of bearing capacity under the existence of seepage flow. From the results of laboratory experiment and theoretical analysis, it was confirmed that the pop-out phenomenon happens and the bearing capacity of rubble mound can considerably decrease due to the tsunami-induced seepage flow. It is concluded that the effect of seepage flow in the rubble mound should be taken into account when making a design of the caisson type composite breakwater against tsunami.