In Japan, a country at the forefront of population ageing, significant geographic variation has been observed in inpatient medical expenditures for older adults aged 75 and above (IMEP75), both at the small- and large-area levels. However, our understanding of how different levels of administrative (geographic) units contribute to the overall geographic disparities remains incomplete. Thus, this study aimed to assess the degree to which geographic variation in IMEP75 can be attributed to municipality-, secondary medical area (SMA)-, and prefecture-level characteristics, and identify key factors associated with IMEP75. Using nationwide aggregate health insurance claims data of municipalities for the period of April 2018 to March 2019, we conducted a multilevel linear regression analysis with three levels: municipalities, SMA, and prefectures. The contribution of municipality-, SMA-, and prefecture-level correlates to the overall geographic variation in IMEP75 was evaluated using the proportional change in variance across six constructed models. The effects of individual factors on IMEP75 in the multilevel models were assessed by estimating beta coefficients with their 95% confidence intervals. We analysed data of 1,888 municipalities, 344 SMAs, and 47 prefectures. The availability of healthcare resources at the SMA-level and broader regions to which prefectures belonged together explained 57.3% of the overall geographic variance in IMEP75, whereas the effects of factors influencing healthcare demands at the municipality-level were relatively minor, contributing an additional explanatory power of 2.5%. Factors related to long-term and end-of-life care needs and provision such as the proportion of older adults certified as needing long-term care, long-term care benefit expenditure per recipient, and the availability of hospital beds for psychiatric and chronic care and end-of-life care support at home were associated with IMEP75. To ameliorate the geographic variation in IMEP75 in Japan, the reallocation of healthcare resources across SMAs should be considered, and drivers of broader regional disparities need to be further explored. Moreover, healthcare systems for older adults must integrate an infrastructure of efficient long-term care and end-of-life care delivery outside hospitals to alleviate the burden on inpatient care.