One of the passengers, who is now admitted to the district hospital, said they were looted, beaten up and then thrown out of the train by unknown persons.
Police found two bodies near Belakoba railway station, few km away from New Jalpaiguri, this morning while seven other persons were found lying injured near the tracks.
"The two had died on the spot. We do not know the reason behind the incident. We are investigating the matter," said New Jalpaiguri area manager (rail) Partho Sarthi Seal.
The injured have been admitted to the district hospital and the North Bengal Medical College Hospital.
Protesting against the incident, locals staged a rail blockade delaying many local trains and all Assam-bound express trains.
Later in the day, the blockade was lifted.