To make well-informed choices, consumers need access to reliable and clear messages regarding the benefits of functional substances in food. This study identified foods with function claims (FFCs) in Japan that had a gap between actual labeling and efficacy information of functional substances not visible on their food package. Between April 1, 2015, to July 20, 2018, 1,310 FFCs were submitted to the regulatory agency and analyzed. The proportion of FFCs with a gap was highest in the health claim category of blood pressure management (79.5%), followed by neutral fat reduction in blood (75%) and suppression of blood sugar spikes (73.4%). These gaps are attributable to differences in food development strategy. Thus, to ensure the quality of benefit communication on FFC to consumers, scientific evidence regarding health claims of functional substances should be managed in an integrated manner.