On June 10, Japan will allow foreign visitors to enter the country on group tours (and only group tours) and travel throughout the country.
According to The Points Guy who spoke to the Embassy of Japan:
This information is always subject to change, so be sure you are checking with the official Embassy of Japan or Counsel General’s office here.
The bottom line is if you are interested in booking a tour group visit to Japan, book ASAP! Spots will begin to full up quickly.
I don’t have any information as to what constitutes a ‘certified agency’ as of yet, but I will post as soon as I have more information.