Japan has a reputation for trains running on time. Trains usually come on time, however, that is not to say there are no delays. In the area around Tokyo, there were 40,600 instances of cancellations and delays over 30 minutes last fiscal year (1 April ~ 31 March). These figures include the knock-on effect as well. Sadly, and reflecting the lack of very strong religious or social taboo associated with it in Japan, 21,100 cancellations and delays were due to people committing suicide, and 7,200 were due to signal failure and other problems with the infrastructure.
Source (Japanese/pdf): http://