Background: The Foods with Function Claim was introduced in Japan in April 2015 to make more products available that are labeled with health functions. A product’s functionality of function claims must be explained by the scientific evidence presented in clinical trials (CTs) or systematic reviews, but the quality of recent CTs is unclear. The purpose of this study was to evaluate the risk of bias (RoB) using “a revised tool to assess risk (RoB 2)” published in 2018 for notifications based on all recent CTs published on the Consumer Affairs Agency website. Methods: A total of 38 submitted papers based on CTs that were published on the Consumer Affairs Agency website during the period from 1 January 2023 to 30 June 2024 were eligible. The RoB 2 tool provides a framework for considering the risk of bias in the findings of any type of randomized trial. This tool with five domains was used to evaluate the quality of research methods. Results: Eligible CTs were assessed as “low risk” (11%, n = 4), “medium risk” (13%, n = 5), and “high risk” (76%, n = 29). A number of highly biased papers were published. Bias occurred in all five domains, especially “bias in selection of the reported result (Domain 5)”, which was the most serious (“high risk”; 75%). For elements correlated with RoB, there was no significant difference (p = 0.785) in the RoB 2 score between for-profit and academic research in the author’s affiliated organization. There was no significant difference (p = 0.498) in the RoB score between the published year categories of 2000–2019 and 2020–2024, and no significant difference (p = 0.643) in the RoB score between English and Japanese language publications. Conclusion: Overall, the quality of the latest CTs submitted after 2023 was very low, occurring in all five domains, and was most serious for “bias in selection of the reported result (Domain 5)”.