Originally Posted by
aresef
The annoying thing is that the smallest bill is 1000 yen. Expect to have a whole lot of coins weighing down your pockets when all is said and done.
An Advice from a local resident.
When you buy a JR ticket at a vending machine, put as many coins as possible first, then notes if necessary and buy it. You can put in all of your coins including 1 yen, 5 yen. They just return those smaller coins and of course the change. The change is given with optimized combination of coins, which you would rather like to have.
This is what I do before I fly abroad.