Spokesman Ronald McInnis says divers found the body Saturday morning inside the train's engine room.
Iron Ore Company of Canada, which owns the train, identified him on Friday as Enrick Gagnon, 45, and said he had worked for the company since 1997.
Parts of the train carrying diesel fuel fell into the Moisie River in eastern Quebec on Thursday, leaving a silvery layer of oil floating on the water.
McInnis says the investigation into the derailment continues.
Iron Ore Company of Canada president Kelly Sanders calls it a "very sad day" for the company.
"Our deepest sympathies and thoughts are with Enrick's family and we will do everything within our power to support them and his co-workers during this difficult time", Sanders said Saturday in a release.
The train was made up of three locomotives and 240 empty cars.
The lead locomotive had a capacity of 17,000 litres and ended up fully submerged in the river.
It was unclear how many litres it contained at the time of the accident near Sept-Iles, about 900 kilometres from Montreal.
The locomotive behind it, which also had a capacity of 17,000 litres, was partially submerged.
An IOC spokeswoman said initial information indicates a landslide caused the derailment in the largely inaccessible area.
A spokesman for the Quebec Environment Department did not know Friday how much diesel was in the river, although he said oil extended for about 20 kilometres out from shore.
Railway traffic on the line remains suspended until further notice.
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