The investigation into a train derailment that killed three Via Rail employees and injured dozens more is progressing slowly, said Via's chief of transportation.

On Tuesday, the train's locomotive was on its way to a secure site where it will be examined by investigators. The hulking and smashed engine car was the last piece of the train to be removed from the site.

The train flew off the tracks on Sunday near Burlington, Ont., tipping on its side and hitting a building. Two longtime Via engineers were killed, along with a trainee who was observing the two veterans.

Dozens more were taken to hospital, where some remain with serious injuries.

Marc Beaulieu, chief of transportation for Via Rail, said the entire company was shaken by the accident but investigators are committed to finding answers.

"We know the derailment site is still being worked on. Most of the train cars have been moved but the investigation is quite slow-paced and we have to be patient," Beaulieu told CTV's Canada AM on Tuesday.

"The TSB (Transportation Safety Board) of course is leading this investigation, we are fully participating to the best of our ability and we can't speculate at this point what occurred, we just have to let the TSB do their job."

Beaulieu said TSB investigators are interviewing witnesses and passengers who were on the train at the time of the crash in order to gather as much information as possible.

Investigators announced Monday they had managed to recover the train's black box, which is expected to reveal information such as how fast the train was going when it crashed and whether the brakes were applied or the whistle was blown.

On Monday, TSB investigator-in-charge Tom Griffith told reporters the train was switching tracks when it derailed.

While Via Rail passenger trains must typically observe a speed limit of 128 km/h in the area where the crash occurred, they are required to slow to 24 km/h while switching tracks.

The black box is expected to reveal whether that happened.

Faisal Abid, a passenger who was riding in the first passenger car of the train, said it felt as though the locomotive was moving much faster than 28 km/h.

"We wouldn't have flown that far, that was pretty hardcore, the seats were all broken inside, the glass was all shattered, I mean people really flew," Abid told CTV News.

Via Rail has identified the three engineers as longtime employees Peter Snarr and Ken Simmonds, and engineer-in-training Patrick Robinson.

Snarr, 52, and Simmonds, 56, were both from the Toronto area and both had more than 30 years experience as engineers with Via Rail and CN.

Forty-year-old Robinson, of Cornwall, Ont., was a new employee at Via Rail and was observing the engineers as part of his training program.

Griffith said it isn't clear which engineer was at the controls when the accident took place. Robinson could have been driving the train, but only under the supervision of the more experienced engineers, he said.