It may not be where you thought.
According to the Ministry of Economics, Trade and Industry, factory and workshops have been closing down fastest in the Tokyo Metropolitan District. In between the end of the year 2000 and the end of 2005, an incredible 28.0% of all TMD factories and workshops (fabrication facilities employing fewer than 3 persons) closed their doors.
During that same period of time, the population of the TMD grew 4.2%--more half a million persons.
A lot of service jobs opening up in Tokyo, it seems.
Other prefectures with significant percentage losses over the end 2000 - end 2005 period include:
Gifu - 23.7%
Nara - 23.5%
Osaka - 23.4%
Interesting in the above map is the position of Aichi among the top ranks of prefectures in terms of percentage of closures. If any part of Japan could preserve the many-layered pyramid of suppliers and sub-contractors, one would think it would be the home of Toyota Motors.
Also interesting are the contrasting fates of the Chūgoku Region and Shikoku. In Shikoku, manufacturing has basically collapsed. In the Chūgoku is has stayed relatively steady (let me be the first to say that the Nikkei's scaling is damn suspicious). If the graph is not entirely misleading, one might hazard a guess that exports to China have something to do with the relatively better survival rates of the Chūgoku region factories.
Another general rule--if you were an economic basket case to begin with, you did not lose nearly as many factories percentage-wise (yes, I'm talking about you, Hokkaidō)--unless your name is Akita, the prefecture with the highest suicide rates of all Japan.
Shizuoka's stability is understandable, given its role as the Tokaidō's industrial underbelly.
Shiga's is an untold story. The prefecture is doing something right--aside from the southern Kantō, Aichi, Fukuoka and those happy breeders down in Okinawa, Shiga is the only prefecture that has been consistently gaining population. It is also holding on to its factories.
Whatever romantic notions one may hold of Japan's true economic strengths, the country sure as heck was not clinging to a monozukuri culture during the Koizumi years. Indeed in general, the healthier the economy of a prefecture, the faster it was disposing of its factories.
The Nikkei's choice of subject and time frame is somewhat amusing. On the very same day, METI released figures showing that for the first time in 15 years total employment in manufacturing grew year-to-year in 2006.
Ken Worsley over at Japan Economy & News Blog has already offered his take on the 2006 numbers.