From August 5th, 2020, those who left Japan with re-entry permission (included special re-entry) before their destination countries were designated as an area subject to denial will be able to apply to return to Japan. Those eligible will have to obtain a “re-entry confirmation letter” from the nearest Japanese Embassy or diplomatic agency.
Submitting evidence of a negative corona virus test conducted within 72 hours of their flight is also required.
Please contact with your local Japanese Embassy for more details.
https://www.mofa.go.jp/ca/fna/page4e_001074.html
https://www.mofa.go.jp/ca/fna/page25e_000334.html
2020年8月5日より、入国拒否の対象地域に指定される以前に再入国許可（みなし再入国を含む）をもって出国した外国人は、日本への帰国申請をすることができます。
対象者は最寄りの日本大使館または関連機関から「再入国確認書」を発行してもらう必要があります。また、渡航72時間前に取得したコロナ陰性証明書の提出も必要です。