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Evidence on the indirect health impacts of disasters is limited. We assessed the excess mortality risk associated with the indirect health impacts of the 2011 triple disaster (earthquake, tsunami and nuclear disaster) in Fukushima, Japan.The mortality rates in Soma and Minamisoma cities in Fukushima from 2006 to 2015 were calculated using vital statistics and resident registrations. We investigated the excess mortality risk, defined as the increased mortality risk between postdisaster and predisaster after excluding direct deaths attributed to the physical force of the disaster. Multivariate Poisson regression models were used to estimate the relative risk (RR) of mortality after adjusting for city, age and year.There were 6163 and 6125 predisaster and postdisaster deaths, respectively. The postdisaster mortality risk was significantly higher in the first month following the disaster (March 2011) than in the same month during the predisaster period (March 2006–2010). RRs among men and women were 2.64 (95% CI 2.16 to 3.24) and 2.46 (95% CI 1.99 to 3.03), respectively, demonstrating excess mortality risk due to the indirect health effects of the disaster. Age-specific subgroup analyses revealed a significantly higher mortality risk in women aged ≥85 years in the third month of the disaster compared with predisaster baseline, with an RR (95% CI) of 1.73 (1.23 to 2.44).Indirect health impacts are most severe in the first month of the disaster. Early public health support, especially for the elderly, can be an important factor for reducing the indirect health effects of a disaster.