Police and railway authorities remained tightlipped on the identity of the attacked passengers, who hailed from Assam, pending an investigation.
Special trains were operated by Railways from Bangalore to ferry passengers fleeing the city over fears of attacks on them sparked by rumours in the wake of Assam violence.
The police found two bodies and the seven injured persons near the tracks at Belakoba railway station, a few km from New Jalpaiguri station.
"The two had died on the spot. We do not know the reason behind the incident. We are investigating the matter," New Jalpaiguri area manager (rail) Partho Sarthi Seal said.
Railway sources quoting one of the injured passengers admitted to the district hospital said they were looted of their belongings and beaten up severely before being thrown out of the train by unknown persons.
The injured have been admitted to the district hospital and the North Bengal Medical College Hospital.
A large number of people blocked train movement at the New Jalpaiguri station in protest against the incident as a result of which some Assam-bound express trains and local trains were stranded.
Later in the day, the blockade was lifted.
The Railways announced an ex-gratia of Rs 15,000 each to the two dead passengers and ex-gratia of Rs 500 each to the seven injured.
The kin of the passengers, who hailed from Hailakandi district in Assam and had confirmed tickets upto Guwahati, would be given the amount, Divisional Commercial Officer (DCM) of Katihar Division of East Central Railway B K Mishra said.
