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Japanese people tend to all take their holidays at the same time, so some periods (Golden Week, Obon, Silver Week) are extremely busy, with zero availability for most touristic cities on all booking websites (Jalan, Goo, JTB, Booking, etc).

Even when all websites show all places as fully-booked, is there still hope to find any accommodation?

Japanese language is not a problem.

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Have you checked out Airbnb? It's pretty big here. – Mazyod Mar 27 at 13:24
    
@Mazyod: It did not even cross my mind! Maybe worth an answer, including your tips and other similar sites if any? – nic Mar 27 at 14:45
    
I don't have much to say, I've pretty much jumped around Airbnb and now staying in a shared house, called Sakura house. Shared houses are abundant as well. I do hope you have a great trip! – Mazyod Mar 27 at 15:16
    
I have never ever encountered a case where a whole city was fully booked. Heck, even in Kyoto for the whole Golden Week (Apr 29-May 5) there are still plenty of available rooms. – fkraiem Mar 28 at 2:23
    
@fkraiem: Details in chat :-) – nic Mar 28 at 2:33

Many small hotels (self-described as minshuku or ryokan) are not bookable through the Internet. Such hotels often have availability even long after all of the Internet-bookable options have sold out.

Booking is made by phone. Obviously, this require knowing some Japanese, as very few have English-speaking staff.

The main difficulty is to find these small hotels that often have no Internet presence. Here is the best way I have found:

  1. Go to the Japanese yellow pages website: http://itp.ne.jp
  2. Type the name of the city you want to stay at
  3. In the left bar, choose 旅行宿泊 (tourism accommodation)
  4. Choose 地図検索への切替 to switch to map mode
  5. Zoom to downtown, as some minshuku can be in very remote places far from public transportation
  6. You get a list of hotels in the desired area
  7. Open each hotel name in a search engine
  8. Filter out the hotels for which the search engine shows Jalan/etc (because you have already searched through these websites)
  9. The search results might have some blogs or pictures of the hotel, and price information
  10. Call the ones that seem OK. It might take 2 or 3 tries before you find one with availability.

As pointed out by Mazyod, another option is AirBnB, they might have different occupation patterns than usual forms of accommodation, because some people rent their place precisely while they go on vacation.

One other solution can be urban camping, which is tricky but feasible in Japan with a bit of attention. If travelling with a low-cost airline, remember that tents might not be allowed as cabine luggage.

A last resort is cited by Wikivoyage:

24-hour comic book library/internet cafes known as manga kisa, are common [...]. This is one of the cheapest ways to crash [...]. No bed, but you have a comfy chair and a PC and/or DVDs if you can't sleep. Later in the evening, karaoke boxes often offer discounted prices for the whole night, they usually have a couch you can sleep on. Most of these cyber cafes charge ¥1500–2500 for 8 hours.

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3  
+1. And a tip: in smaller towns, the tourist information office (almost always at or right next to the train station) will be happy to call on your behalf. Don't expect them to do this for you in Tokyo or Kyoto though! – jpatokal Mar 28 at 2:25

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