While vaccines are pivotal in combating COVID-19, concerns about side effects and complex procedures have hindered complete vaccination. Prior studies suggest that individuals defaulted to opt-out exhibit higher COVID-19 vaccination rates compared to those in opt-in systems. However, these studies were conducted in countries with a tolerant attitude towards vaccination and default changes, targeting specific age groups, and did not address potential deterrents like the increase in cancellation rates on the day, discomfort towards changing defaults, or the possibility of the opt-out effect being a one-time occurrence. Under the hypothesis that the default nature of the COVID-19 vaccination system influences attitudes towards vaccination even in countries conservative about vaccination and default changes like in Japan, we aimed to examine the differences in the first and second dose vaccination rates, cancellation rates, and the number of complaints between the opt-in and opt-out systems for COVID-19 vaccination. An email survey was conducted in 10 cities in A Prefecture, Japan. The results showed not only higher COVID-19 vaccination rates across all comparable age groups in the opt-out group but also a notably smaller decrease in the second-dose vaccination rate compared to the opt-in group, all achieved without any complaints about the system’s introduction. Consequently, it can be inferred that the potential inhibiting factors were largely overcome. Despite some limitations, such as regional specificity, the study suggests that opt-out systems might increase COVID-19 vaccination coverage without leading to significant cancellations or complaints, presenting a promising strategy to facilitate vaccination efforts.