Pros & cons of Asian buying:

This relates to my personal experiences of buying in Asia.
You can decide how well it extends to Japan specifically.

I have visited Asia frequently in recent years - although not Japan (China, Hong Kong, Malaysia, Singapore, Brunei, ... ). Pricing is generally competitive in the best cases but not stunningly better in most cases and it's easy to pay more than western prices if not careful. Prices on ebay from Asian sources are usually as good and sometimes better than the best you can find "on the street", with an occasional stunning exception. I was in Kuala Lumpur in mid 2011 when D700's were offered at about $500 less than the going rate elsewhere. I didn't buy one. I shall mourn forever :-).

Products may be "grey market". These are often genuine products that have come from sources that do not have official manufacturer sanction, for whatever reason. You need to be aware of which products are or aren't grey market and whether this has any implications for you.

Some manufacturers offer international warranties on product bought in another country. Some don't. it may vary by product for a manufacturer.
Sony offer international warranty if you visit their offices in the country of purchase after purchase and fill in appropriate forms. (I bought a Sony A700 and SAL18250 lens in Hong Kong and registered them on this basis).

Sellers lie and misrepresent in some cases. This happens anywhere, but you may have slightly better hope of redress if the seller is in your own country rather than far far away. Maybe not. (I bought a Compaq laptop (not a camera, I know :-) ) in Hong Kong and the seller misrepresented the warranty - it turned out to be a "refurbished" model with 6 months warranty). It failed out of warranty BUT when I complained to Hewlett Packard they honored the warranty that I had been told I had. I'd expect that in most cases camera manufacturers would not be so accommodating.

Firmware / Software versions may differ and you may have to apply the correct update for your version. This may be available, may be described in a language you can understand and may have all the same features as the ones available in your market (or more). Or not.

Resale value may be affected.