Two of the injured were passengers on the train, and the third was the driver of the tractor.
Quebec provincial police Sgt. Joyce Kemp said the accident happened at the level railway crossing at 3rd Line Road.
She said the road remains closed to traffic as the investigation continues.
There were 220 passengers aboard the Amtrak train, bound for New York. Kemp said they were transferred to buses to continue their journey by road.