A flap-gate breakwater is a new type structure for coastal disaster reduction against tsunamis and storm surges. The breakwater usually lies down on the seabed and rises up as a seawall with its buoyancy when tsunami or storm surge occurs. In our previous experimental studies, wave blocking capabilities of the flap-gate against tsunamis were confirmed, and the characteristics of the gate motion and wave pressure have been clarified changing wave condition. Present study develops a numerical model considering fluid-body interactions for the flap-gate and validation of the numerical model is conducted. The numerical model consists of combining the overset grid method and level set method for solving both flap-gate motions and free surface water motions accurately. It is shown that the developed numerical model gives accurate predictions of flap-gate motions against hydraulic model experiments.