There are many discounted ticket shops in Japan, some are close to train stations.
For example, I go to Ashiya, Hyogo Pref. very often and I usually use this ticket shop close to the JR Ashiya Station to buy discounted tickets.
For example, from Ashiya to Osaka, the rate is JPY300, but you can buy the same ticket with JPY220 or so.
However, this kind of discounted tickets have some limitation for use.
It can be used from 10:00 through 17:00 and weekends only.
You can also find "discount ticket vending machine" like this.
According to this article, there are a couple of hundreds of discounted ticket vending machines in Japan and 60% of them are in the Kansai area (West Japan).
(http://style.nikkei.com/article/DGXNAS18ABF01_V10C14A2AA1P00)
It's all in Japanese, so if you're interested in buying discounted tickets from vending machine, it would be a good idea to study some Japanese before coming to Japan.