On March 9, 2021 the government of Japan announced that it has decided to further strengthen its border measures and if those who enter Japan on or after March 19, 2021 are unable to submit the inspection certificate, you will not be allowed to enter Japan based on the Quarantine Law.
【https://www.mhlw.go.jp/content/000753086.pdf 】

However, due to the current situation, those who have difficulty to obtain a COVID-19 negative certificate will not be subject to boarding refusal and will be able to enter Japan by possessing the "Consular Letter" issued by the Embassy.
【https://www.mm.emb-japan.go.jp/profile/japanese/news/2021/new-71.html】

(Note) If you are boarding an ANA direct flight, you do not need to obtain a consular letter as the procedures will be carried out by the Embassy. Only those who board a transit flight need to obtain a consular letter.

Therefore, we would like to inform you that the "Consular Letter" issued by the Embassy will be handled as follows.

The application of the "Consular Letter" will be accepted even if the flight is not confirmed.

●How to apply:　
Please apply by email (ryoji@yn.mofa.go.jp) to the Consular Section of the Embassy.
Please write “Application for a consular letter” in the subject line of the email.

●Reception Period:　
Until two days before boarding (Monday to Friday)

●Attachment:　
Passport (A copy of the face photo page)
Flight number (All including transit flights)
※If your flight has not been confirmed yet, please indicate approximate date when you will enter Japan.

●Delivery Date:　
Business day following the date of receipt

●Fee:　
Free of charge