Ocean robots that equipped with manipulator for building underwater structures and handling investigations of ocean resources have been studied. To achieve high-precision and high-speed positioning for the manipulator, its vibration caused by an additional mass effect of fluid, a drag force and a buoyant force, etc. should be evaluated by vibration tests in water in actual equipment and suppressed through this evaluation. However, the vibration tests of the underwater structures (we refer to machines and structures in water as underwater structures) to measure frequency response function are difficult. This paper proposes a method of a non-contact experimental vibration analysis using pulsed-laser ablation for the underwater structures that were completely submerged in water. The impact testing with impulse hammer is used widely for experimental vibration analysis due to the simplicity of the apparatus. However, the impact testing has limitations in use in underwater condition because it is difficult for experimenters to operate the impact hammer in water. The proposed method yields the frequency response functions by applying a pulsed-laser-ablation excitation force to the structure and measuring the output using a laser Doppler vibrometer. Since the direction, strength and effective duration of the pulsed-laser-ablation force are essentially constant, this force can be calibrated by measuring these properties in advance. Therefore input-detection-free frequency response function measurements can be realized. The results obtained in this study demonstrate the effectiveness of the present vibration test method for the underwater structures.