No-pictures buildings in Japan (shooting from street forbidden by law)

The only case I'm aware of where it's actually illegal to photograph something from a public place is when that something is a US military base or affiliated facility in Japan. Here's the Mutual Cooperation and Security Treaty under Article VI Facilities and Areas and the Special Criminal Act Attendant upon the Enforcement of the Agreement Regarding the Status of United States Armed Forces in Japan (phew!):

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Basically, violating the "confidentiality" (??) of a US Army base by providing "documents, diagrams, etc" with a "purpose" of harming the Army is punishable by up to ten years in prison.

Now you might well reasonably object that that doesn't say anything about photography, but this is apparently how the bases' well-posted ban is justified. And if you're tempted to argue the point with the military police who'll come stop you if you try, bear in mind that Article 2 of the same law also makes it an unambiguous crime not to GTFO promptly when told to do so, with a maximum penalty one year in prison.

And, while I can't prove a negative, that's it, although I understand a similar restriction applies to Japanese army self-defence forces bases as well. There are plenty of owner-imposed restrictions on indoor photography in private places, and the aforementioned privacy restrictions that make publishing identifiable photographs of anybody tricky, but neither of these is a matter of criminal law. (Assuming, again, that you cease, desist & leave when told to do so and thus don't become a trespasser.)