To be technically accurate, to my knowledge it's impossible to enter Japan from any country without a visa. However, if you come from certain countries (basically any western country, plus various others), they will automatically give you a 90-day tourist visa when you land, so it's effectively "visa free". Otherwise, you have to apply for a visa and get that in your passport before you arrive.
"On Sept. 7, the government allowed those on nonguided tours who had booked their flights and hotels through registered travel agencies." ← is the "through registered travel agencies" portion dropped now as well? I couldn't discern that from the article.