It depends on the hotel. Many cheaper and better places can be booked up though, especially during weekends and peak seasons, so doing it ahead of time online would be smart. Look at the hotel website or booking engine like hotels.com etc.
I would say booking on your own accord on the Internet. A great deal of hotels in Japan not only have a website of their own with English booking, but many have also put up an entry on popular accomodation booking websites such as Booking.com, Jalan, Japanican, Rakuten Travel and Agoda.
We booked last year 2 weeks Expedia this year booked Hotels .com as i booked 42 rooms for 3weeks 2 rooms for 4 every night.as very small most hotels not fit 4 people comfortably. got 4 free nights for next vacation .
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Look at the hotel website or booking engine like hotels.com etc.