The decision, which will come into effect from June 25 and apply on basic fare, comes nearly a week after Prime Minister Narendra Modi said the country should be ready for "tough decisions".
Due to the hike, a passenger will now have to shell out Rs 4354 for a journey between Delhi and Kolkata by AC-I on Delhi-Howrah Rajdhani, instead of Rs 3813.
Journey between Delhi and Mumbai by Rajdhani will cost Rs 4073 instead of Rs 3567 in AC-I, Rs 2357 instead of Rs 2064 in AC-II and Rs 1617 instead of Rs 1416 in AC-III.
Travel between Delhi and Chennai by Delhi-Chennai Rajdhani will now cost Rs 4673 instead of Rs 5430 in AC-I, Rs 3129 instead of Rs 2740 in AC-II and Rs 2119 instead of Rs 1856 in AC-III.
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Today's decision marks implementation of an announcement of May 16, the day Lok Labha election results came, when the hike was announced but put on hold immediately.
Announcing the decision, less than a month after the NDA government took over, Railway Minister Sadanand Gowda said, "I was forced to implement the order that was done by my predecessor. I am only withdrawing the withholding order."
He said the interim budget presented by the previous government had assumed certain revenues on the basis of the proposed hike that was announced on May 16.