I'm not sure if most people know but you need to distinguish between two kinds of trains here.

The Shinkansen system is rarely late, that is true. Part of the reason for that is that they are running on their own, isolated tracks. Downside here is that they are quite expensive. Flights between, let's say Tokyo and Osaka, are often faster and cheaper.

The trains that normal people take every day to get to work, are, depending on city and line/owner of course, partially late every single day during rush hour. They don't even show the time or kind of the next train that will come.

The commuters of course know this and just leave the house a bit earlier, so in practice it's not a huge problem.