There is an active startup culture in Japan but it is quite different than in the Valley. It is influenced by the culture, laws and history of the people here. The foreigners living in Japan also bring their culture and have their own interesting relationship. It's a very complex subject.
Here's a good presentation that can give you an overview of the web startup space:
http://www.slideshare.net/araipiyo/situation-and-recent-tren...
Japan's GDP is about 1/3 of the US, yet according to your link there was only $0.2 Billion of venture investment, as compared to $17.7 B in the U.S. That's roughly 1% of US venture Financing and wildly disproportionate!
There seems to be something holding back entrepreneurship, and I don't think its for lack of smart people.
One particularity in Japan, I don't know if that matters that much: working for a big company is still regarded as the quasi only way to get a career in Japan.
Then again, maybe I'm not looking hard enough.