The problem of high-level disorganization seems to be the biggest long-term challenge facing Japan’s institutions.

Oh their probably organized, but more along the "nursing home" model.

Noah Smith is one of the greatest idiotological clowns posing as an economist. There is no high-level disorganisation in Japan, anyone who knows anything about Japan knows that things are too organised. And the level of organisation and red tape is so entrenched and complex that meaningful decisions, and quick action are impossible.

Limping along I guess you could be organized.

People within individual departments are extremely organized but usually only communicate with whoever they consider essential to their position. So you haven't enough cross-communication and this creates departments and institutions which live in their own bubbles. Is it the tendency to not think outside the box, or not wanting to attract attention, or simply protecting their turf? Maybe all of the above.