If you ride in the first car and look at the timetable the driver uses, you can see the timetable is accurate to the second.
Here's a photo showing a driver's timetable. In the second row is a 20 second stop at Hazama, the train arrival time is 13:25:05 and departure 13:25:25.
That timetable looks like it's on 5-second granularity, not 1-second. Which is still pretty tight -- the UK's working timetables are half-minute granularity. (The UK also demonstrates that it's not merely a matter of having an exact timetable, you also need to be able to keep to it in practice :-))
Here's a photo showing a driver's timetable. In the second row is a 20 second stop at Hazama, the train arrival time is 13:25:05 and departure 13:25:25.
http://livedoor.blogimg.jp/asianrailroad/imgs/f/a/fa9e3956.j...