The genomics community has long acknowledged the lack of diversity in datasets used for research, prompting various stakeholders to confront this issue. In response, the Global Alliance for Genomics and Health (GA4GH) formulated a policy framework that recognizes the multiplicity of perspectives on diversity and proposed a systemic approach for more optimal data diversity. Given the importance of the research context, assessing this policy’s applicability within countries where diversity is less discussed is important. This study investigated the feasibility of implementing the GA4GH policy in Japan, a nation with a smaller genetic diversity than many Western countries. As the proportion of East Asian genomic research is limited internationally, focusing on the Japanese genome contributes to enhancing diversity. Meanwhile, labelling findings as “Japanese” can inadvertently reinforce perceptions of homogeneity and overlook ethnic minorities. Regions and socioeconomic status are also recognized as substantial factors of diversity within academia, yet concerns persist among the public regarding the heritability of stigmatized conditions. Social inclusion of sexual minorities has begun in Japan, but research surveys generally still use binary sex and gender categories, which underscores the need for additional variables. This study found that both academia and the public need to confront the overemphasis on homogeneity within Japanese society and hesitancy in addressing genetic factors. By doing so, more inclusive and diverse datasets can advance the field both ethically and scientifically. Perhaps the most important impact of the GA4GH policy will be to draw greater attention to the complex diversity challenges ahead in Japan.