By comparing mutations found on the butterflies collected from the different sites, the team found that areas with greater amounts of radiation in the environment were home to butterflies with much smaller wings and irregularly developed eyes.
"It has been believed that insects are very resistant to radiation," said lead researcher Joji Otaki from the University of the Ryukyus, Okinawa.
"In that sense, our results were unexpected," he told BBC News.
The team concluded that this higher rate of mutation came from eating contaminated food, but also from mutations of the parents' genetic material that was passed on to the next generation, even though these mutations were not evident in the previous generations' adult butterflies.
The team of researchers have been studying that particular species butterfly for more than 10 years. They were considering using the species as an "environmental indicator" before the Fukushima accident, as previous work had shown it is very sensitive to environmental changes.