The agency obtained a search warrant this week to help it determine whether all safety rules were followed. The rules and regulations are set out in the Railway Safety Act and the Transportation of Dangerous Goods Act.
"Transport Canada is carrying out its investigation at the offices of Irving Oil in Saint John, New Brunswick," a spokesperson for Transport Minister Lisa Raitt told CBC News Friday.
An Irving spokesman confirmed the company had been contacted by Transport Canada but said "operations remain normal."
"We have received requests from government investigators regarding our operations. We continue to fully co-operate with them, complying with all requests for information," Sam Robinson told CBC News in an email.
Crude oil on a train was destined for Irving's refinery in Saint John when cars derailed and exploded in the Quebec town, killing 47 people.