Upscale hotels, Business hotels, Dormitories, Youth Hostels are diff types of lodgings available in Japan
Tokyo has many diff types of lodging facilities..
It has the upscale 3 star or 5 star hotels like Ritz Carlton and Hyatt etc.
Then there are business hotels like Hotel Villa Fontaine, Park Inn etc which are in the range of 7000 JPY - 10000 JPY depending on season etc.
Then there are service apartments at reasonable price from Space design, Oakwood, Duplex etc which are again centrally located, have the comfort of home + hotel.
Then there are shared dormitories like Sakura house - http://www.sakura-house.com/en/ which is very cheap and can be used for survival..
Then here you can also find a list of all youth hostels in Japan - http://www.hihostels.com/dba/cmap-JP.en.htm?linkid=980028 - if you are member of youth hostel in your homecountry then you can use it again at reasonable rates.