This study proposes a probabilistic methodology for estimating the business interruption loss of industrial sectors as an extension of current methodology. The functional forms and parameters are selected and calibrated based on survey data obtained from businesses located in the inundated area at the time of the 2000 Tokai Heavy Rain in Japan. The Tokai Heavy Rain was a rare event that hit a densely populated and industrialized area. In the estimation of business interruption losses, functional fragility curves and accelerated failure time models are selected to estimate the extent of damage to production capacity and production recovery time. Significant explanatory variables, such as inundation depth, distinct vulnerability, and the resilience characteristics of each sector, as well as the accuracy of fit of the model, are analyzed in the study. The function obtained and the estimated parameters can be utilized as benchmarks in estimating the probabilistic distribution of business interruption losses, especially in the case of urban flood disasters.