Without a direct split between iphone and ipod, there is no way of telling which device the Japanese are using. Are they sticking with their advanced mobiles and using the ipod touch, or are they switching to the iphone?
Apple have (worldwide) sold 34m iphones, 17m of them to the US and 17m to the rest of the world, Japan has 120 million people, 3% of 17m is 510,000, doesn't really seem so impressive like that does it, Apple selling 510,000 phones in Japan. But again, without knowing the exact figures of the split between iphone/ipod then it's just a rough percentage guess.
However if you look at:
It gets broken down pretty well, Apple may hold 46% market share for smartphones, but in Japan smartphones are a tiny market, Apple doesn't even break out of the "other" category which have a total market share of 22.6% (others that is, not Apple on its own).
So in summary, the iphone market in Japan is tiny, lumping it in with the ipod to seem like it has higher growth than it has is pretty terrible.