Descriptive observational studies showed upward jumps in secular European perinatal mortality trends after Chernobyl. The question arises whether the Fukushima nuclear power plant accident entailed similar phenomena in Japan. For 47 prefectures representing 15.2 million births from 2001 to 2014, the Japanese government provides monthly statistics on 69,171 cases of perinatal death of the fetus or the newborn after 22 weeks of pregnancy to 7 days after birth. Employing change-point methodology for detecting alterations in longitudinal data, we analyzed time trends in perinatal mortality in the Japanese prefectures stratified by exposure to estimate and test potential increases in perinatal death proportions after Fukushima possibly associated with the earthquake, the tsunami, or the estimated radiation exposure. Areas with moderate to high levels of radiation were compared with less exposed and unaffected areas, as were highly contaminated areas hit versus untroubled by the earthquake and the tsunami. Ten months after the earthquake and tsunami and the subsequent nuclear accident, perinatal mortality in 6 severely contaminated prefectures jumped up from January 2012 onward: jump odds ratio 1.156; 95% confidence interval (1.061, 1.259), P-value 0.0009. There were slight increases in areas with moderate levels of contamination and no increases in the rest of Japan. In severely contaminated areas, the increases of perinatal mortality 10 months after Fukushima were essentially independent of the numbers of dead and missing due to the earthquake and the tsunami. Perinatal mortality in areas contaminated with radioactive substances started to increase 10 months after the nuclear accident relative to the prevailing and stable secular downward trend. These results are consistent with findings in Europe after Chernobyl. Since observational studies as the one presented here may suggest but cannot prove causality because of unknown and uncontrolled factors or confounders, intensified research in various scientific disciplines is urgently needed to better qualify and quantify the association of natural and artificial environmental radiation with detrimental genetic health effects at the population level.