Demanding an immediate roll back of the hike, they said the massive increase in passengers fares would fuel inflation further burdening the common people.
Scores of Congress workers, led by party's Delhi unit president Arvinder Singh Lovely, held a demonstration in West Delhi slamming the Narendra Modi government for increasing the fares bypassing Parliament.
The protests caused traffic snarl-ups as police used water cannons when the demonstrators tried to break the barricades.
"People who used to talk about 'achche din' (good days) before the elections are now talking about bitter medicines," Lovely said.
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He threatened the Congress would launch a "rail roko" stir if the decision was not rescinded.
The Delhi unit of the CPI(M) also staged a protest outside the Rail Bhawan.
Clashes erupted between Samjwadi Party and BJP workers in front of the Uttar Pradesh legislative assembly in Lucknow with the rival groups hurling stones at each other over the hike in rail fares.
The BJP alleged the SP workers tore down their posters and pelted stones at the party office while the latter charged the saffron party activists with hurling bricks at them.
"Though 3 or 4 policemen were injured in the clash, we have no report of injuries from either side," SHO Hazratganj said.
Elsewhere in the state, Congress and SP workers squatted on rail tracks, chanted slogans against the Central government and demanded an immediate roll back of the hike.