In an announcement dated 12 June 2020, the Japanese Ministry of Justice (MoJ) has published exemptions from the general refusal of entry for foreigners who have stayed in a country on the immigration ban list published by the MoJ.
Further information on the entry restrictions and exemptions can be found here: PDF Newsflash
More information about legal implications of the coronavirus can be found here.
The Japanese Government lifts the COVID-19 state of emergency nationwide. Tokyo and four other prefectures (Kanagawa, Chiba, Saitama and Hokkaido) were the last regions where the emergency state has been removed. Entry restrictions to Japan for foreign nationals still remain. For an updated overview on the actual border enforcement measures, please see the website of the Japanese Ministry of Foreign Affairs under https://www.mofa.go.jp/ca/fna/page4e_001053.html