JSDF Tokyo Vaccination Center
Large scale vaccination center in Tokyo for COVID-19 is located at business district in Chiyoda ward which most of tourists would not visit during their stay in Japan.
The vaccination center is run by JSDF, Japanese Self Defense Force and located inside one of the buildings of Ministry of Defense. It is opened for expats living not only in Tokyo but also living outside of Tokyo. However, you should have the vaccination coupon(voucher) issued by local municipality where you live before making your reservation.
The vaccine which is used here is produced by Moderna, Inc. On the other hand, vaccine used by local municipalities' vaccination center or local hospitals/clinics are by Pfizer. Most of the people living outside of Chiyoda ward visit this center due to reservations for local vaccination centers have not started yet.
The vaccination center is a few minutes away from subway Otemachi station but there is a complimentary shuttle bus from Tokyo station till 23 August.