On October 1, 2020, the Japanese government did ease the entry of foreign students into Japan in a phased manner.
They will be required to undergo a 14-day medical examination before entering the country and a COVID-19 inspection 72 hours prior to entry, and will be required to undergo a 14-day quarantine upon arrival.
This will allow students to study abroad. It is not known at this stage how long this situation will end.
Added on January 21, 2021
The CoE issued in FY2020 is now valid until July 31, 2021.
For more information, please visit the website of the Ministry of Health, Labor and Welfare.
Regarding the validity period of the Certificate of Eligibility (updated 1/21) (excerpt from the above URL)
We are making preparations to allow you to come to Japan in April, but if you would like to change your study abroad start to July, please contact us.
We apologize for any inconvenience this may cause to students who are planning to come to Japan, but we appreciate your cooperation.