Composite materials have attracted significant attention with regard to the manufacturing of structures that require weight reduction, such as automobiles and aircraft, because they are more resistant to corrosion and fatigue than conventional metal materials. However, such materials exhibit a reliability degradation problem, i.e., their mechanical and physical properties deteriorate due to the occurrence of delamination and voids. Ultrasonic inspection methods have been widely applied for nondestructive detection of such defects in structures; however, the application of these approaches has been impeded due to high anisotropy and acoustic attenuation. In addition, the existing ultrasonic inspection methods require considerable time and cost for the inspection of large materials or structures. These problems were addressed in this study by developing an automatic ultrasonic inspection system; this was achieved by adopting a squirter-type water injection device, which uses a multi-joint robot and the through-transmission ultrasonic method. In addition, a software program to correct axis misalignment was developed and verified to solve the deterioration in defect detectability and accuracy that was caused by axis misalignment, which may occur during the use of the developed system. This development was accomplished after measuring the coordinates of the deformed mechanical part using a three-dimensional laser measuring instrument.