If you do not want to stay with other HC members, or noone is available, here is what other members suggest. Hostels Hotels Camping Other Options
Here are some of the budget options :
1. Business Hotels
They offer a single room with futon (and maybe some rooms have TV set) and public bathrooms/toilets, some offers free breakfast, some don't. Price range from JPY2000-JPY3000 per night.
2. Internet Cafe
Some of them offers "night package" of 5 or 10hours, price can drop up to JPY150 per hour (JPY1500 for 10-hour package). You are provided with pillow and blanket, computer with internet connection, tv set with dvd player and some game consoles (PS3, Nintendo, etc). Some provides free shower, but some charges a low fare for the shower room, free flow soft drink from the vending machine, and of course, extensive collections of comics and magazines (Japanese only)
3. Karaoke room
As well as the internet cafes, karaoke rooms charges 'happy hour" packages for night-time usage, and even more cheaper (can be under JPY1000 for 8-hour usage), but you'll have to sleep on the couch, and they only have toilets (no shower rooms of course), with free soft drinks from the vending machine.