Estimating the early internal doses to residents in the Fukushima Daiichi Nuclear Power Station accident is a difficult task because limited human/environmental measurement data are available. Hence, the feasibility of using atmospheric dispersion simulations created by the Worldwide version of System for Prediction of Environmental Emergency Dose Information 2nd Version (WSPEEDI-II) in the estimation was examined in the present study. This examination was done by comparing the internal doses evaluated based on the human measurements with those calculated using time series air concentration maps (131I and 137Cs) generated by WSPEEDI-II. The results showed that the latter doses were several times higher than the former doses. However, this discrepancy could be minimised by taking into account personal behaviour data that will be available soon. This article also presents the development of a prototype system for estimating the internal dose based on the simulations.