Originally Posted by Tokyorich
I just wanted to add. If you miss the train by as little as one minute, the train company rules say that the ticket is no longer valid. A fight at the counter will sometimes help.
That's because if you miss the train by one minute, your train is gone! This is Japan, where things both run on time and your rights are narrowly specified. You bought a ticket for a specific train at a specific time! What do you think, that you can just waltz in on any train at your convenience, bringing meiwaku to everybody else? Bad person! You can't do that on a plane, why could you do that on a train?
Given that, your best bet is probably just to get on the next train, sit on an unoccupied seat, and hope for the best. Train conductors will sometimes just let you "ride", especially if you play clueless gaijin. That's the flip side of Japan. In the US, you'd probably be arrested for "security reasons" since you aren't supposed to be there, hence you must have evil intent.