This study proposes a safety evaluation process for a prevention structure against tsunamis, in which the most updated guideline (i.e. FEMA P-646) is used as the deterministic analysis and a probabilistic approach is adopted to consider uncertainties involved. To overcome the incomplete data on Tsunamis, a Markov chain Monte Carlo (MCMC) simulation is developed to increase the quantity of historical data from Taiwan followed by the use of the least squares support vector machine (LS-SVM) to estimate the probability density function (PDF) of random variables. Based on the fragility analyses of the superstructure, substructure and entire system, if the wall thickness is below 4.45m, the wall thickness is more likely to be the governing factor compared with the pile diameter. Conversely, the pile diameter would more likely be the dominating factor. When the pile size decreases from 75cm to 65cm, the threshold value will shift from 4.45m to 3.85m. In addition, when the wall thickness and height are greater, there is a greater likelihood of the failure probability being governed by the substructure. Based on historical records only, the probability of failure of the seawall is extremely low. Nevertheless, results shown here are in line with the engineering judgement and the computation procedure established in the present study can be used as a reference for performing safety analysis on tsunami structures with insufficient data.