Reliability of vibration analysis of structures in contact with water has been improved in recent years, whereas mechanism of damping due to fluid is not well understood and estimation method of damping due to fluid is not developed for most structures. However, widespread use of computational fluid dynamics is considered to facilitate clarifying the flow around a vibrating structure. Calculation technique such as coupling of fluid analysis and structure analysis is still time consuming and it is also not suitable for understanding the mechanism of damping. It is considered to be more useful to perform structure analysis and computational fluid dynamics separately. The authors have been developing a method to estimate damping due to fluid using computational fluid dynamics and finite element analysis of structures. Some excitation tests of a cylindrical tank separated by a horizontal plate with an opening were carried out in order to validate the damping estimation method. Simplified damping estimation method without utilizing CFD was also developed. Amplitude dependence, the effect of the size of an opening were investigated and compared with estimated results. Also, the possibility to increase damping by horizontal plate with an opening is discussed.