This study was conducted based on the case of an accident (excessive deformation) that occurred during the hydraulic test of a shipboard tank manufactured in accordance with the design regulations. Over-pressure phenomenon was noted as the main cause of accidents in the process of testing tanks without physical damage, which can be found in external factors such as cross-sectional difference between inlet pipe and air pipe and higher water filling rate than the recommended one. The main goal of this paper is to establish a safe water filling rate according to the range of sectional area ratio(SAR) reduced below the regulations for each test situation. The simulation was conducted in accordance with the hydraulic test procedure specified in the Ship Safety Act, and the main situation was divided into two types: filling the tank with water and increasing the water head to the test pressure. The structural safety evaluation of the pressure generated inside the tank and the effect on the structure during the test was reviewed according to the SAR range. Based on the results, guidelines for the optimal filling rate applicable according to SAR during the hydraulic test were presented for the shipboard tanks used in this study.