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Background: In Japan, heated tobacco products (HTPs) are promoted by the tobacco industry as reduced-risk tobacco products despite the lack of evidence for this claim. This study determined the distribution of HTP-harmfulness perception and identified the explanatory factors associated with the perception of HTP as less harmful than conventional cigarettes. Methods: A nationwide cross-sectional survey was conducted with Japanese people aged 20 years or older (INFORM Study 2020) using a self-administered questionnaire. We performed descriptive analysis and weighted logistic regression analysis to examine the relationship between explanatory factors (eg, individual characteristics, socioeconomic status, and trusted sources of cancer information) and the perception of HTPs as less harmful. Results: Among 3,420 participants, the proportions of those who perceived HTPs as less harmful were 40.3% and 18.3% for users and non-users of tobacco, respectively. For participants aged 20–39 years, the proportions were 49.9% and 30.4%, respectively. Among 1,160 tobacco non-users who were familiar with HTPs, male, aged under 39 years, and having lower education were associated with the perception of HTPs as less harmful. Trusted sources of cancer information were not associated with the perception of HTPs as less harmful. Conclusion: This study showed that, among tobacco non-users, being male, aged under 39 years, and having lower education were associated with a perception of HTPs as less harmful. Public health stakeholders should provide the latest evidence about HTP harmfulness in their daily practice and strengthen the regulations on HTP marketing directed at both tobacco- and tobacco non-users.