Especially in Tokyo and Kyoto
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When I visited Tokyo in 2008 I used several websites. Here are some links.
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Actually there are lots of cheap hotels in Japan. All you have to do is to search it in the internet for more information and reservations.
Here's a list of every Cheap Hotel in Tokyo.
How to have a cheap vacation in Tokyo:
Shinagawa has plenty of cheap accommodation, especially if you book online for an extended time period:
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