Gaffe-prone Grant Shapps said the tragic Stonehaven crash site looked like a "Hornby train set thrown up in the air".
Driver Brett McCullough, conductor Donald Dinnie and passenger Christopher Stuchbury were killed when a ScotRail service came off the tracks in Aberdeenshire after heavy rain on August 12.
Union bosses slammed the UK Transport Secretary's "glib remarks" in response to Labour pressing about privatisation and UK suppliers in the rail industry.
Speaking in the Commons, Mr Shapps said: "I went to the scene of the tragedy.
"I was taken over in a helicopter. It was like a Hornby train set thrown up in the air."
Shapps was forced to quit the Cabinet in 2015 over a Tory bullying scandal.
And last month he gave the wrong day for the France quarantine rules - throwing travel plans into chaos.
He added: "And our thoughts and prayers are with, not just the three who died, but those who were injured and the emergency workers and the brave people who rescued them.
"Our thoughts are with them all.
"The House will have noticed that I issued the Network Rail interim report on Stonehaven a week or two back which comes to some very important interim conclusions and I'll update the House further with the full report shortly."
Network Rail said the train hit a pile of "washed-out rock and gravel before derailing".
Kevin Lindsay, Aslef's organiser in Scotland, criticised Mr Shapps for his comments.
He said in a statement: "It is unfortunate in the extreme that the Secretary of State for Transport should make such a glib remark.
"This was a real accident, involving real people - three of whom died, and six of whom were injured - and a real train.
"It was not a Hornby model train set thrown up in the air in a Tory Government minister's playroom.
"Mr Shapps really should think more carefully about what he says and how he says it.
"Because he is treading on the feelings of the families and friends and colleagues of those who died."
