We quantitatively analysed the relationship of health literacy with both anxiety about the COVID-19 outbreak and free-text qualitative data. A questionnaire was mailed to 5450 citizens aged 16–89 years in four prefectures between late April and May 2020. It gauged the level of anxiety about COVID-19, assessed health literacy (HL) on both critical and communicative HL subscales, and invited free-text responses. We compared anxiety levels in three groups of both HL subscales. Text-mining analyses were also conducted among the three HL groups. Two-thirds of respondents reported anxiety about COVID-19, and 42% of them also reported fear. The level of communicative HL was negatively associated with no or low anxiety (p < 0.01), and the same association was observed for critical HL (p < 0.01). Free-text analysis identified 11 categories related to concerns about COVID-19: response of the national government, appreciation of health care practitioners, early convergence, vaccine development, fear of infection, invisible, a school for children, everyday life, information-related issue, novel coronavirus and self-quarantine. Words that were characteristic of the high-HL group were ‘information’, ‘going out’, ‘vaccines’ and ‘government’. This survey reveals high public anxiety under COVID-19, and while anxiety is associated with HL levels, people with higher HL may make more prudent and healthier decisions. In situations of uncertainty, different approaches to alleviate anxiety depending on HL are warranted, providing new insights and contributing to public health measures during the outbreaks.

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