BackgroundIn the context of the COVID-19 pandemic, limited research has focused on socioeconomic disparities in Local Healthcare System Efficiency (LHSE) among Japanese prefectures. This study seeks to investigate the moderating impact of vaccination on the relationship between LHSE and socioeconomic characteristics and endowmentsMethodsTo explore these relationships, we first utilized the Data Envelopment Analysis with Slack-Based Measure to measure the LHSE, based on data from Japanese prefectures during waves 2 to 5 of the pandemic. Then estimating the impact of socioeconomic variables on LHSE. Finally, we assessed the changes in the way socioeconomic variables affect LHSE before and after vaccine deployment using the Seemingly Unrelated Estimation t-test methodology.ResultsThe research findings suggest an overall reduction in LHSE disparities across various regions due to the utilization of vaccines. Particularly in areas with relatively nsufficient bed resources, a significant improvement in LHSE was observed in most regions. However, there was no evidence supporting the role of vaccine deployment in mitigating socioeconomic inequalities in LHSE. Conversely, the utilization of vaccines showed a positive correlation between the improvement in LHSE and the proportion of older adult population in regions with sufficient bed resources. In regions facing bed shortages, the enhancement of LHSE became more reliant on reducing the occupancy rate of secured beds for severe cases after the introduction of vaccination.DiscussionIn regions facing bed shortages, the enhancement of LHSE became more reliant on reducing the occupancy rate of secured beds for severe cases. This underscores the importance for policymakers and implementers to prioritize the treatment of severe cases and ensure an effective supply of medical resources, particularly secured beds for severe cases, in their efforts to improve LHSE, in the post-COVID-19 era with rising vaccine coverage.