Due to the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident, the evacuees from Namie Town still cannot reside in the town, and some continue to live in temporary housing units. In this study, the radon activity concentrations were measured at temporary housing facilities, apartments and detached houses in Fukushima Prefecture in order to estimate the annual internal exposure dose of residents. A passive radon–thoron monitor (using a CR-39) and a pulse-type ionization chamber were used to evaluate the radon activity concentration. The average radon activity concentrations at temporary housing units, including a medical clinic, apartments and detached houses, were 5, 7 and 9 Bq m −3, respectively. Assuming the residents lived in these facilities for one year, the average annual effective doses due to indoor radon in each housing type were evaluated as 0.18, 0.22 and 0.29 mSv, respectively. The average effective doses to all residents in Fukushima Prefecture due to natural and artificial sources were estimated using the results of the indoor radon measurements and published data. The average effective dose due to natural sources for the evacuees from Namie Town was estimated to be 1.9 mSv. In comparison, for the first year after the FDNPP accident, the average effective dose for the evacuees due to artificial sources from the accident was 5.0 mSv. Although residents' internal and external exposures due to natural radionuclides cannot be avoided, it might be possible to lower external exposure due to the artificial radionuclides by changing some behaviors of residents.