If you like high-level material that's questionably formatted -
and who doesn't - check out the relevant wiki page:
http://shadowrun.wikia.com/wiki/Japanese_Imperial_StateIt's not terribly up-to-date but they can give you some of the basics. More importantly, it can also act as a good bibliography, although the posters here have also done a good job summarizing things.
The Sixth World Almanac is nice but only has about three pages on Japan.
Shadows of Asia has ~20 pages but it's now 12 years old and might not be what your GM is using.
Corporate Enclaves has 55 pages on Japan, but it's specific to Neo-Tokyo rather than to Japan in general.
As others have mentioned, it might be easiest to sit down with your GM and talk with him/her about what books they're using and how they envision Japan. They might even be able to loan you the relevant materials.
Have fun!