Americans seem to have this thing where they think Asians are shorter than White people to a significant degree. It's not true. Yeah sure, there are very short Asians, and very tall White people, but the reverse is true as well. Statistically, there is a noticeable, but small difference - and it's steadily decreasing. Yet some people continue to ask silly questions like "Do you bang your head everywhere?", etc. No, of course not - not any more than I would in the US.
This is common sense to me, knowing a lot of Asians in the US, and having spent a lot of time in Asia, but I decided to quantify it a bit.
So let's have a look at the mean heights for males and females in the US and Japan:
Data from Wikipedia.
For the metric impaired, that's 1.4 inches for guys and 1.3 inches for girls. Not much of a difference, especially when you take into account that the variance of height of individuals is much greater than this. There is also evidence that the difference is decreasing due to a convergence of diets between countries as the world becomes a smaller place. So are Japanese people shorter? Statistically speaking, yes. Enough shorter to matter? No.