Assumed that you are living in Thailand and plan to come to Japan for business purpose. Even if you hope to come to Japan for sightseeing, as of now, you can not acquire short term visa in principle.
Thailand is designated as Travel Warning Infectious Diseases Level 2.
(In the website of government of Japan, there is information in English language. However it publicized only old information. So when you look for necessary information, you need to refer to information written in Japanese language)
So you can use method of “Residence Track paper”.
Residence track paper is a kind of written pledge, declaration paper.
Resident of Japan (a person or company who invites you to Japan) promises it will observe you when you are in Japan.
It needs to know where you stay and move and manage you.
(If you are from Singapore, South Korea, Vietnam, you can use Business track paper and it is less regulated)
(Before departure from Thailand)
In the case you come to Japan with Residence track, while you are Thailand, you need to monitor your health condition for 14 days and make a record. So you need to monitor body temperature for 14 days.
(But you do not need to get PCR test in your home country. So it is merit of Residence Track system.)
And you need to apply for short term business visa to embassy of Japan in Thailand.
You also need to show written pledge.
(You promise you take necessary quarantine process and never make fake statement)
(At the airport in Japan)
When you arrive at airport in Japan, you need to submit a paper that clarifies your health condition (you can receive necessary paper on the plane) and written pledge.
And you are recommend to install applications to your smartphone that trace your movement in Japan.
(Between airport of Japan and your hotel in Japan)
You can not use public transportation for 14 days (So you can not use train) and need to stay in same place for 14 days (So you can not move around Japan within 14 days)
This process is not applied to a person who has status of residence in Japan.
When you come to Japan, you need to join insurance that covers medical expense in Japan.
You need to install map application software that can record your location in Japan for 14 days.
Other than Thailand, Australia, Singapore, Republic of Korea, China (including Hong Kong and Macau), New Zealand, Brunei, Vietnam and Taiwan are designated as Level 2.
The receiving company/person (company/ person that can assure observation of quarantine measures) is requested to fill in “Written Pledge (=Residence Track)”.
Information for Permanent Resident of Japan who can not return to Japan due to Covid-19
Conclusion : You can take necessary process at Consulate general of Japan in your home country.
Assumed that you are permanent resident of Japan. However you are staying in your home country now and can not return to Japan due to corona virus.
When you departed from Japan, you applied for re-entry permit or deemed re-entry permit.
However while you can not return to Japan, valid period of your re-entry permit lapsed.
In that case there are 2 options. (as of December 2020)
1)You can visit Consulate general of your current country and extend valid period of Re-entry permit (Not Deemed re-entry permit).
2) In the case you can not extend your Re-entry permit or you have deemed re-entry permit.
And valid period of permit is after 1st January 2020 until 6 months after the “day” you can return to Japan legally.
(“day” = when the country is removed from denial of landing.)
In this case you can visit Consulate general of Japan in your home country and apply for visa of “Long term Resident”.
Then you can come to airport in Japan and take necessary process to acquire status of residence of permanent resident.