Abstract Purpose: Excess deaths during the COVID-19 pandemic have become an issue in Japan, which has a rapidly aging population, and we conducted this study to evaluate how age-adjusted mortality rates for individual cancers shifted during the pandemic. Methods: Using published national data, we compared age-adjusted mortality rates for each cancer type between the first 3 years of the pandemic (2020-2022) and the 3 years before the pandemic (2017-2019), and also compared mortality rates in 2022 after nationwide mRNA-LNP vaccination to rates in 2020 before vaccination began. In addition, we identified trends in mortality from 2012 to 2019 to assess excess/deficit mortality during the pandemic. Results: Age-adjusted mortality rates decreased from the pre-pandemic period to the pandemic period for stomach, liver, lung, gallbladder/biliary tract, colon, and esophageal cancers, which account for a large proportion of cancer deaths in Japan, but this decreasing trend slowed from 2021 to 2022. Age-adjusted mortality rates for breast, pancreatic, lip/oral/pharyngeal cancers and leukemia increased significantly in 2022 after much of the Japanese population had received the third mRNA-LNP vaccine dose, compared to 2020, the first year of the pandemic when no vaccinations were administered. There were also marginally significant increases for ovarian and uterine cancers between 2020 and 2022. Data interpretations: As previously described in a molecular biological study, the increased mortality rates for these cancers might be caused by cell proliferation mediated by binding of spike protein to estrogen receptors, and the spike protein might originate from mRNA-LNP vaccination rather than COVID-19 infection itself. The significance of this possibility warrants further studies.