There was a great article in the Economist a while back about this:
http://www.economist.com/node/14793432
Since this article was published, the situation has gotten worse. The earthquake sure didn't help, but the situation wasn't good even before that. Sure, 10% or something of the parts that go into the iPhone are developed by Japanese specialized parts manufacturers, who have skills that no-one else in the world can match. But if you look more closely, you'll see that these industries are hollowing out -- there isn't enough interest from younger generations to keep the mom&pop shops going in the long run.
The problem which many have mentioned here and elsewhere is that while Japan is unrivalled in craftsmanship ("monozukuri") -- making physical things -- exactly the opposite is true when it comes to "unphysical" things like software. That's why Japanese mobile phones have such utterly terrible interfaces, as someone else pointed out here. There is very little respect given to that side of the design process, and that's not going to change without a major shift of consciousness.