After chemical, biological, radiological, nuclear or explosive (CBRNE) disasters, trepidation and infodemics about invisible hazards may cause indirect casualties in the affected society. Effective communication regarding technical issues between disaster experts and the residents is key to averting such secondary impacts. However, misconceptions about scientific issues and mistrust in experts frequently occur even with intensive and sincere communications. This miscommunication is usually attributed to residents’ conflicts with illiteracy, emotion, value depositions and ideologies. However, considering that communication is an interactive process, there are likely to be additional factors attributable to experts. This article aims to summarize the gaps in rationality between experts and residents observed after the 2011 Fukushima nuclear disaster to describe how residents perceived experts. There were discrepancies in the perception of ‘facts’, the perception of probability, the interpretation of risk comparison, what were included as risk trade-offs, the view of the disaster, whose behavior would be changed by the communication and whether risk should be considered a science. These findings suggest that there was a non-scientific rationality among residents, which often exercised a potent influence on everyday decision-making. It might not be residents but experts who need to change their behavior. The discrepancies described in this article are likely to apply to communications following any CBRNE disasters that affect people’s lives, such as the current COVID-19 pandemic. Therefore, our experiences in Fukushima may provide clues to averting mutual mistrust between experts and achieving better public health outcomes during and after a crisis.