"The Japan Railways Group, more commonly known as JR Group (JRグループ Jeiāru Gurūpu?), consists of seven for-profit companies that took over most of the assets and operations of the government-owned Japanese National Railways on April 1, 1987. Most of the liability of the JNR was assumed by the JNR Settlement Corporation." - https://en.wikipedia.org/wiki/Japan_Railways_Group

In short, they just agreed to give up a small bit of their own profits.