North East Frontier Railway (NEFR) sources said the blast occurred at 0130 hrs in the train's first compartment which was a parcel van and had railway staff and a large number of illegal passengers.
Police said a programmable timed device was planted allegedly in the compartment by some among the illegal passengers, who alighted from the train at Morioni.
The blast did not damage the tracks and the driver managed to take the train to nearest Bokajan station.
The injured were rushed to the Dimapur civil hospital where the condition of 12 was stated to be very critical.
Police suspected Adivasi militants to be behind the incident as they had been active in Tinsukia-Dibrugarh region from where the train originated.
Meanwhile, the railway authorities have stepped up security arrangements throughout the railway stations and lines as various groups, demanding reservation, were likely to target the trains and stations.