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There is a small number of JR trains that partially use the railway tracks of different railway companies. If you travel along such sections with a Japan Rail Pass or Seishun 18 Kippu, a supplement fee has to be paid for the non-JR section. This supplement is usually paid to the conductor on board of the train or at a station.

The map and list below show the non-JR sections most likely encountered but not easily identified as such by foreign tourists. Note that there are several other such sections in addition to the ones listed below.

  Non-JR section Affected trains Fee
1
Morioka - Koma
Iwate Ginga Railway
Local trains along the JR Hanawa Line use the railway tracks of the Iwate Ginga Railway between Morioka and Koma. 650 yen
2
Osaki - Tokyo Teleport - Shin-Kiba
Tokyo Waterfront Area Rapid Transit
Trains on the JR Saikyo Line that continue to run on the Rinkai Line, a popular line that connects to Odaiba and Shin-Kiba. 330 yen (Osaki - Tokyo Teleport)
3
Ito - Izukyu Shimoda
Izukyu Express
Local and limited express trains to/from Izukyu-Shimoda Station. Note that unlike the Japan Rail Pass, the JR Tokyo Wide Pass and the various other JR East passes are valid on this section. 1620 yen
+510 yen for limited express trains
4
Naoetsu - Joetsu Myoko - Arai
Echigo Tokimeki Railway
Rapid and limited express trains between Niigata and Arai that connect to the Hokuriku Shinkansen at Joetsu Myoko Station. Note that unlike the Japan Rail Pass, the JR East Nagano Niigata Area Pass is valid on this section. 240 yen (Naoetsu - Joetsu Myoko)
+210 yen for limited express trains
5
Kanazawa - Tsubata
IR Ishikawa Railway
Local and limited express trains from Kanazawa in direction of Wakura Onsen on the Noto Peninsula. But note that Japan Rail Pass and Seishun 18 Kippu holders can ride the IR Ishikawa Railway between Kanazawa and Tsubata if they don't get on and off in between (to access the JR Nanao Line). 270 yen
+200 yen for limited express trains
6
Kawarada - Tsu
Ise Railway
Local trains and the Mie rapid trains between Nagoya and Toba via Ise. Limited express trains from Nagoya down the Kii Peninsula in direction of Kumano. 510 yen
+310 yen for limited express trains
7
Fukuchiyama - Toyooka
Kyoto Tango Railway
Limited express trains from Kyoto to Amanohashidate. 1420 yen (unreserved)
1520 yen (reserved)
8
Kamigori - Chizu
Chizu Express
Local trains and limited express trains from Kyoto and Okayama to Tottori. Note that unlike the Japan Rail Pass, the JR Sanyo Sanin Area Pass and JR Sanin Okayama Area Pass are valid on this section. 1300 yen
+520 yen for limited express trains
9
Kubokawa - Wakai
Tosa Kuroshio Railway
Local trains between Uwajima and Kubokawa. 210 yen

Page last updated: April 1, 2016