The workers blocked the Kanyakumari-bound Island Express from Bangalore at nearby Aluva station and raised slogans against the rail fare hike.
Police arrested the activists against whom Railway Protection Force registered cases, RPF sources said.
They also blocked the Palakkad-Ernakulam train at the North railway station, railway police said.
Similar protest was also held in Thiruvananthapuram Central station.
The protesters, led by Dean Kuriakose, state Presidet of Youth Congress, demanded roll back of the fares, police said.
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