"special exceptional circumstances" for being not to refuse landing was updated on September 1st.

It has been widely reported in the news and other sources that the Immigration office has started operations to allow re-entry to foreigners with a resident status on September 1.
As a result, if one has a resident status now, one can re-enter to Japan.

In addition, an important change was made to the "Regarding denial of landing to prevent the spread of COVID-19" on September 1.
The article is here（http://www.moj.go.jp/content/001327502.pdf）

１、The important change

That is "2 Regarding special exceptional circumstances - (3)".

(3) Foreign nationals who departed from Japan with a re-entry permit before August 31 and who were not permitted to re-enter Japan because the validity period of the re-entry permission expired after the country/region of stay was designated an area subject to denial of landing (Note 3).

Even if one has a re-entry permit (including deemed re-entry permit) and one's resident status has expired already while the landing refusal, one can re-enter to Japan.

The important point here is that the expiration date of a re-entry permit is usually one year in the case of a deemed re-entry, but to be precise, it is  "from departure to one year or the expired period of a resident status".

Of course, if the period expires, the re-entry permit will also expire.

Therefore,this (3) also applies to foreigners who have not been able to re-enter Japan due to the landing refusal and their period of resident status has expired.

This has already been confirmed by phone at the Immigration Bureau.

２、Entry conditions

Note 3 is attached to this (3).
This is quoted below.

(Note 3) Depending on the purpose of your entry, you may need to get a Certificate of Eligibility at the regional immigration bureau and get Japan Visa at the Japanese embassy/consulate in the country/region.

In other words, one must have a Certificate of Eligibility in order to re-entry.

Issuance of the Certificate of Eligibility has already started as usual, and applications for the issuance of a Certificate of Eligibility for one whose resident status has expired due to the landing refusal are operated by express (very fast).

Therefore, the conditions of Note 3 are not so severe.

３、Conclusion

Due to the operation change on September 1st, even if one's resident status has expired while going out Japan due to the landing refusal, one can enter to Japan through an entry procedure at a Japanese embassy if one has a Certificate of Eligibility.

This is the same as a new entry, but unlike the new entry that only started in Vietnam and Thailand, it is treated specially.

In addition, for the re-entry, a negative PCR test certificate within 72 hours of the scheduled departure date is currently required.
For more information, please contact your local Japanese Embassy abroad.

Normally, the immigration office is harsh, but regarding this, they help foreigners who have lost their resident status due to the landing refusal and have no choice, in line with the mitigation of re-entry that began on September 1.

It is contrary to the principle of equality that the timing of re-entry is different from those who happened to overlap with the landing refusal and those who did not, so it is natural to say that it is "of course".
But the "of course" is very difficult for Japanese government offices.
I think the Immigration office did a good job this time.

I sincerely hope that such a kind operation like this will be carried out continuously.