Okay, I did a little checking and I can relate this story, because it’s all outdated now. Yay!
Anyway, I was providing security for a nuclear weapons transfer to a secure bunker in Germany. I went to check the inside of the bunker (it was a great big underground place, not some little pill-box) and was wandering around when I noticed a big rusty iron trap-door in the floor of the storage room. Naturally I was a bit curious as to where it went, so I asked the guards. They basically said, “Trapdoor? What trapdoor?”, and when I pointed it out to them it turned out that they hadn’t ever really noticed it before. So there was a considerable amount of checking with various people in charge, and it turned out that of the few people who actually had noticed the door, they each thought that somebody else had checked it out and taken care of things.
So, we very very carefully pried open the door and took a peek inside, and there was a nice shaft and ladder leading way down into a big tunnel. It turned out that in WWII, the Germans had made a huge series of underground defensive structures and tunnel network under the whole city, and had just sealed it up when they abandoned it and everybody forgot about it. I got to go down the tunnels and explore around to find out where they led to (which was great fun, since the Germans had a habit of leaving unfriendly little surprises in such places). I ended up finding a second entrance to the place, which led up into the sub-basement of some guy’s house on the other side of town. He didn’t know anything about it since it was covered over in old plaster, and was a bit startled to have a bunch of armed soldiers wander out of his cellar.
And this wasn’t just some little backwoods town, either, but an actual great big thriving city with a big tunnel network and all sorts of chambers and things under it. So I can see why Tokyo might have a similar thing, especially considering that at the same time the Germans were building theirs Tokyo was being frequently fire-bombed.