The freight train was towing 240 cars and three locomotives when it derailed Thursday due to an apparent landslide.
Gagnon, 45, was found on Saturday morning inside the train’s engine room, inside the lead locomotive that ended up completely submerged in the Moisie River.
His Facebook page lists him as being from, and living in, Sept-Îles, Que.
Gagnon had worked for the Iron Ore Company of Canada, the owner of the train, since 1997.
However, according to Innu Chief Réal McKenzie, the incident could have been far worse had Thursday been like any other day.
Passenger train normally goes first
Mackenzie, the chief of the Innu nation in Schefferville, said three different trains use the Quebec North Shore and Labrador Railway.
He said the passenger train from Sept-Îles to Schefferville usually leaves first on Thursday mornings, while the freight train waits.
Mackenzie doesn’t know why the empty cargo train left the station first ahead of the passenger train this week.
He said the engineer had no way of knowing about the landslide that caused the derailment because it happened overnight.
The train requires two kilometres of track to stop, making it impossible to avoid derailing, Mackenzie said.
He said the passenger train would have certainly met the same fate had it gone ahead of the freight train.
"There were 45 passengers on board," Mackenzie said, referring to the passenger train.
Fuel leaked into Moisie River
The train's lead locomotive had a capacity of 17,000 litres and ended up fully submerged in the Moisie River.
The locomotive behind it, which also had a capacity of 17,000 litres, was partially submerged.
It was unclear how many litres it contained at the time of the accident near Sept-Îles, about 900 kilometres from Montreal.
A spokesman for the Quebec Environment Department did not know how much diesel was in the river, although he said oil extended for about 20 kilometres out from shore.
An IOC spokeswoman said initial information indicates a landslide caused the derailment in the largely inaccessible area.
Divers were unable to get into the water on Friday because it was too dark after the land near the river had been declared safe.