UPDATE Sept. 22, 2022: JAPAN WILL NO LONGER REQUIRE VISAS AS OF OCTOBER 11, 2022. As of October 11, Japan will resume visa-free entry to nationals from qualifying countries. Individuals traveling to Japan after this date DO NOT need to obtain an ERFS and visa to enter the country for individual tourism. The information below is for posterity and/or people who wish to travel to Japan prior to this change going into effect.

UPDATE Sept. 12, 2022: News media is reporting rumors of an imminent announcement which may include the reinstatement of visa waivers. Such an announcement would make most of the information below obsolete. Travelers who do not need visas immediately are advised to wait until we know more.

Overview

Until further notice, a visa is required from all foreigners to enter Japan. The visa-waiver program which previously allowed visa-free entry to nationals from certain countries has been suspended. In order to obtain a visa, a receiving agency must sponsor your application by issuing you an ERFS (Entrants, Returnees Follow-up System) certificate. ERFS certificates may be issued for a variety of reasons, including tourism, in which case a licensed travel agency must sponsor your visa application.

Tourism

As of September 7, 2022, tourists may enter Japan on unguided, unaccompanied tours as long as they are sponsored by a travel agency who arranges their flights and accommodations and acts as a point of contact for the duration of their stay in the country in the event of issues including a COVID infection. Some official documents from the Japanese government have attempted to clarify this policy (and, most notably, what it means for a receiving agency to "arrange" flights and accommodations), however in practice it has been left up to the interpretation of the sponsoring agencies. Due to the lack of clarity, there is a range of interpretations with some agencies insisting on purchasing all airfare and hotel reservations on behalf of the traveler, with others allowing travelers to keep their existing reservations as long as they share the details with them. The exact offerings and pricing from specific agencies is changing rapidly, consult this thread for the latest information.

As of now there have been no reports of denied visas or entry into the country from anyone who had a valid ERFS from a legitimate travel agency. Individuals from Australia have reported difficulties booking visa appointments, so Aussies may want to contact their local consulate and ensure they can do so before paying for a tour package/ERFS.

Visa Application and Arrival Process

The following roughly outlines the steps for obtaining a visa and entering the country:

1. First, the traveler must obtain an ERFS certificate from their sponsoring agency. Who issues the ERFS depends on the reason for entering the country (business travelers should obtain it from the company they are visiting, tourists should obtain it from a travel agency who is arranging their visit, etc.). The ERFS certificate is a one-page document summarizing key information about the traveler and their sponsor. An example of an ERFS certificate is provided here.
2. Once the ERFS is obtained, travelers must apply for a visa from their local Japanese consulate. Travelers from some countries (currently only the USA and Canada) may apply for an eVisa online. This process is faster and easier than physically visiting a consulate so it is recommended for anyone who has access to it.
3. Visitors who are fully vaccinated with three doses of approved vaccine do not need to obtain a COVID test prior to traveling to Japan. A primary series consisting of one dose of J&J/Janssen is treated as two doses for the purpose of meeting these criteria (see here). Vaccination information should be submitted using the MySOS app and travelers should ensure they have a "blue screen" in the app prior to boarding their flight. Information available here.

Frequently Asked Questions

Q: What other documents are required for the visa application? Do I need an itinerary document?
A: For an eVisa application you only need to submit your ERFS and passport. No other supporting documentation is necessary. In-person applications may ask for more documentation and you should verify what documents are required with your local consulate.

Q: What documents are required to board a plane and enter the country?
A: Travelers who have reported their experiences have said they were asked to show their MySOS "blue screen" and their visa/eVisa by both the airline (prior to boarding their flight) and by customs (after landing in Japan). If you have an eVisa, make sure you can load the digital version of the actual eVisa website on your phone (not just the PDF) in Japan over data or WiFi, because these have a rotating QR code.

Q: What if I don't want to stay at a hotel and want to stay at a friend's house/Airbnb/couch-surfing/etc.?
A: Current tourism guidelines suggest that a travel agency is supposed to "arrange accommodations" for your time in Japan. As such, you should contact your travel agency to ask them what types of accommodations in Japan they will allow. It is advisable to book a hotel in Japan for at least your first night in the country prior to applying for a visa since the visa application asks for this information. Note that hotels in Japan are currently very cheap, especially with the weakened Yen.

Q: What if I'm not traveling for (x) amount of time? When should I get an ERFS and apply for a visa?
A: Visas are only valid for 90 days after they are issued, so you should wait until your trip is at least within the next three months. There is also a good chance that the Japanese government will move to further relax entry requirements (including, possibly, re-instating the visa-waiver program which would make this entire process obsolete) in the coming months, so you should wait until your individual planning process requires you to have some assurance that you'll be able to enter the country. We may also see more competition among travel agencies offering bare-bones tour packages in the coming weeks, which could drive prices down.