As of the end of November, 2021, the rate of completion for second-dose COVID-19 vaccine administration was almost 80% in Japan. We evaluated waning COVID-19 vaccine effectiveness in Japan, controlling for mutated strains, the Olympic Games, and countermeasures. The effective reproduction number R(t) was regressed on current vaccine coverage and data of a certain number of days prior, as well as shares of mutated strains, and an Olympic Games dummy variable along with data of temperature, humidity, mobility, and countermeasures. The study period was February, 2020 through November 4, as of November 25, 2021. Estimation results indicate that vaccine coverage of more than 90 days prior raises R(t) significantly. Especially, vaccine coverage with 90 or 120 days prior cancelled vaccine effectiveness completely. Results indicate significant waning of vaccine effectiveness from 90 days after the second dose.