Objective The interim evaluation of Health Japan 21(second term), a national health promotion plan, suggested that improvements in the food environment did not lead to improvements in individual dietary habits. The present study aimed to evaluate the relationship between the dietary behavior targets of Health Japan 21 (second term) and perceived food environment and health literacy.Method We conducted an online cross-sectional survey in March 2019 among adults aged 20-64 years. From the 9,667 registered monitors of the research firm, we collected 2,851 responses (29.5% response rate). The perceived food environment (how people perceive the local food environment) was estimated using the following six questions, namely, availability: easy access to nutritionally balanced meals, accessibility: no inconvenience in daily shopping, affordability: access to nutritionally balanced meals at reasonable prices, accommodation: easy access to food services within business hours, acceptability: satisfaction with the quality of food ingredients, and another form of acceptability: adequate food safety. Health literacy was evaluated using five questions related to information gathering, information selection, information transfer, information judgment, and self-determination. Last, we asked the respondents about two dietary behaviors, namely, the frequency of a balanced diet (defined as comprising the staple food, a main dish, and a side dish) and the quantity of vegetable intake, along with sociodemographic information. The analysis included 2,111 respondents, excluding those whose socioeconomic status was unknown. Multiple logistic regression analyses were performed to determine the relationship between perceived food environment and health literacy on dietary behaviors, while adjusting for sociodemographic factors.Result A balanced diet was associated with the following perceptions of the food environment: "access to nutritionally balanced meals at reasonable prices" (adjusted odds ratio [95% confidence interval] = 1.37 [1.02, 1.82]; women), and "adequate food safety" (1.54 [1.19, 1.98]; men), and health literacy: "information gathering" (0.84 [0.73,0.97]; men) and "self-determination" (1.28 [1.10,1.50], 1.37 [1.14,1.63]; men, women). The quantity of vegetable intake was associated with the following perceptions of the food environment: "easy access to nutritionally balanced meals" (1.54 [1.15,2.06]; men), and "no inconvenience in daily shopping" (1.55 [1.12,2.15]; women), and health literacy: "information transfer" (1.30 [1.10,1.54]; men), and "self-determination" (1.67 [1.38,2.02]; women)).Conclusion To achieve a balanced diet and increased vegetable intake in a population, it is necessary to promote both the acquisition of a higher level of "self-determination" (rather than "information gathering") in health literacy and the creation of a heathy food environment.