I don't know Japan but the author has a whole paragraph about how it's not the case, and how a big part of Japan success comes from the fact that this is not the case, so the author must be wrong one way or the other:

> Unlike other countries, Japan simply returned to the traditional private railway model of the nineteenth and early twentieth centuries: tracks, trains, stations, and yards were owned by vertically integrated regional conglomerates.

> There are substantial advantages to vertical integration. Railways are a closed system that has to be planned as a single unit. Changing the timetable at station A can affect the timetable at station Z; buying new trains that can travel faster might require changes to the infrastructure so they can reach their top speed, which in turn requires rewriting the timetables. This becomes especially complicated if different services share tracks. To prevent delays from propagating from one service to another, the timetable needs to be carefully designed to make best use of the available infrastructure.

> […]

> By maintaining and restoring the institutions that built the first railway systems in the nineteenth century, the Japanese have created the mightiest railway system of the twenty-first.