Bdnews24.com said the train had just left Akhaura junction when the robbers attacked.
The bandits threw the passengers out while the moving train was passing over Bhadughar bridge in Brahmanbaria, Bdnews24.com reported.
Survivor Rubel Mia of Kalacherra village said seven or eight robbers boarded the train at Pagachong station early Thursday.
"They threw us off the train when we resisted them," she said.
The robbers took valuables and cash, Bdnews24.com said.
Police said two passengers, a man and a woman, died, while three injured passengers were admitted to the hospital. Two of those passengers later died.