Japan gets mixed marks in terms of ease of travel for those with disabilities. On the plus side, many new buildings have access ramps, major train stations have lifts, traffic lights have speakers playing melodies when it is safe to cross, and train platforms have raised dots and lines to provide guidance for the visually impaired. You'll find most service staff will go out of their way to be helpful, even if they don't speak much English.
On the negative side, many of Japan's cities are still rather difficult to negotiate, with many narrow streets lacking pavements.
Major sights take great pains to be wheelchair friendly and many have wheelchairs you can borrow for free. Note, however, that 'accessible' at traditional sights (like castles and temples) might still mean steep slopes or long gravel paths. Often the accessible routes aren't obvious; tell staff (such as those at the ticket counter) that someone in your party is travelling in a wheelchair (車椅子; kuruma-isu) and you may be led around to some secret back corridors.
Train cars on most lines have areas set aside for people in wheelchairs. Those with other physical disabilities can use the priority seats near the train doors. You will also find these seats near the front of buses; usually they're a different colour from the other seats.
A fair number of hotels, from the higher end of midrange and above, offer a ‘barrier-free’ (バリアフリー; bariafurii) room or two (book well in advance). Larger attractions and train stations, department stores and shopping malls should have wheelchair-accessible bathrooms (which will have Western-style toilets).
Japan Accessible Tourism Center (www.japan-accessible.com/city/tokyo.htm) is a cheat-sheet for accessible sights and hotels in Tokyo.
Download Lonely Planet's free Accessible Travel guide from http://lptravel.to/AccessibleTravel.