Cancer patients with diabetes experience a poorer prognosis, yet the population burden of this multimorbidity remains unknown. This study aimed to estimate the latest incidence and prevalence of cancer with diabetes mellitus in Japan. We used projection of cancer incidence and latest survival data from population-based cancer registries. The incidence of cancer associated with diabetes was estimated separately for patients with pre-existing diabetes and those without diabetes, and used to estimate the 5-year cancer prevalence for those with and without diabetes. The prevalence of pre-existing diabetes in cancer patients at any cancer site was estimated to be 20.7% (647,160 men and women). Among cancer sites, diabetes prevalence was high in patients with liver and pancreatic cancers in both sexes. In conclusion, our study shows a large burden of diabetes in cancer patients in Japan, which warrants further attention by health practitioners and policy-makers.