When a 'JR line operated in parallel' has become unused because (a portion of) a regular railway line operated in parallel has been abolished or has been transferred to a joint public-private venture railway company (for examples, the section from Takasaki Station to Karuizawa Station to Nagano Station on the Nagano Shinkansen line, the section between Morioka Station and Hachinohe Station on the Tohoku Shinkansen line, and the section between Shin-Yatsushiro Station and Sendai Station on the Kyushu Shinkansen line), the actual route distance is used for the fare calculation.
並行在来線（の一部）が廃止されたり第三セクター鉄道に転換されたりして「並行するJR線」が消滅した区間（長野新幹線の高崎駅-軽井沢駅-長野駅間・東北新幹線の盛岡駅-八戸駅間・九州新幹線の新八代駅-川内駅間）については、実際のキロ数を営業キロとする。