This spring the big news for train lovers was the integration of almost all the regional IC card services, thus making it possible to travel from one region to another on lines operated by different companies using a single IC fare card. But while computer systems have been linked successfully to allow for such inter-line transfers, one element of the changeover that has bothered public officials remained problematic: the non-integration of fares.
In some instances it actually costs more to go from point A to point B using an IC card than it does with a ticket, though most patrons aren't aware of the fact. It depends on which lines you are using. For instance, if you are going from JR Kameari Station on the Joban Line in eastern Tokyo to JR Yokohama station and buy a ticket for the whole trip, it costs you ¥780. However, if you take the same route and use an IC card, ¥910 will be subtracted from your card balance. That's because the Joban line turns into the Chiyoda subway line, which is operated by Tokyo Metro, after it passes Kita Senju, and the passenger then leaves the Chiyoda Line at Nishi Nippori and transfers back to JR in order to proceed on to Yokohama.
The ticket you buy from a vending machine takes these transfers into consideration and simply charges the zone-related JR fare between Kameari and Yokohama plus the Metro fare. But the IC card system doesn't make such a distinction and each of the three legs of the journey is charged separately, meaning you pay two JR fares, one from Kameari to Kita Senju and another from Nishi Nippori to Yokohama, plus the ¥160 for the Chiyoda line between Kita Senju and Nishi Nippori.