After linking to the Associated Press' decidedly unsatisfactory report on discussions of Japan's nuclear reactors and the latent nuclear weapons capability they represent, it is only fair and proper to link to a worthwhile read.
This would be the update from the Nuclear Threat Initiative (NTI) on Japan's civilian highly-enriched uranium (HEU) programs.
Civilian HEU: Japan
Now this is the real deal. Plutonium is nasty stuff and difficult to transform into big bang weapons (just ask the North Koreans). HEU is nasty stuff and way too easy to transform into big bang weapons.
Where does Japan have its HEU? The update page lists four locations.
Yes, I too hope these sites are well guarded.