Especially in Tokyo and Kyoto
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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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When I visited Tokyo in 2008 I used several websites. Here are some links.
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.
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