Apple has yet to roll out any indoor mapping features in Japan so finding the correct route to a train or subway station is a challenge. Directions always steer you to the little station icon on the map which is almost never the station entrance.
Google has had indoor mapping available in Japan for over a year but for some strange reason Google directions ALSO steer you to the little station icon and not the station entrance even thought the indoor data is right there on the screen.
Only Yahoo Japan Maps get it right, for train stations at least. Be careful navigating subway station entrances, none of the majors, Apple, Google and Yahoo Japan, offer accurate directions to entrances.