Background Perinatal mortality increased in contaminated prefectures after the Fukushima Daichi Nuclear Power Plant (FDNPP) accidents in Japan in 2011. Elevated counts of surgeries for cryptorchidism and congenital heart malformations were observed throughout Japan from 2012 onward. The thyroid cancer detection rate (2011 to 2016) was associated with the dose-rate at the municipality level in the Fukushima prefecture. Since the birth weight is a simple and objective indicator for gestational development and pregnancy outcome, the question arises whether the annual birth weight distribution was distorted in a dose-rate-dependent manner across Japan after Fukushima. Methods The Japanese Ministry of Health, Labour, and Welfare provides prefecture-specific annual counts for 26.158 million live births from 1995 to 2018, of which 2.366 million births (9.04%) with weights < 2500 g. Prefecture-specific spatiotemporal trends of the low birth weight proportions were analyzed. Logistic regression allowing for level-shifts from 2012 onward was employed to test whether those level-shifts were proportional to the prefecture-specific dose-rates derived from Cs-137 deposition in the 47 Japanese prefectures. Results The overall trend of the low birth weight prevalence (LBWp) in Japan discloses a jump in 2012 with a jump odds ratio (OR) 1.020, 95%-confidence interval (1.003,1.037),p-value 0.0246. A logistic regression of LBWp on the additional dose-rate after the FDNPP accidents adjusted for prefecture-specific spatiotemporal base-line trends yields an OR per mu Sv/h of 1.098 (1.058, 1.139),p-value < 0.0001. Further adjusting the logistic regression for the annual population size and physician density of the prefectures, as well as for the counts of the dead, the missing, and the evacuees due to earthquake and tsunami (as surrogate measures for medical infrastructure and stress) yields an OR per mu Sv/h of 1.109 (1.032, 1.191),p-value 0.0046. Conclusions This study shows increased low birth weight prevalence related to the Cs-137 deposition and the corresponding additional dose-rate in Japan from 2012 onward. Previous evidence suggesting compromised gestational development and pregnancy outcome under elevated environmental ionizing radiation exposure is corroborated.