It was later revealed the horse had suffered a broken right shoulder and couldn't be saved.
"It is with sadness that we confirm that The Cliffsofmoher had to be humanely euthanised after sustaining a fractured right shoulder during the running of the Melbourne Cup at Flemington", Mr Stier said.
The Cliffsofmoher was an Irish horse ridden by English jockey Ryan Moore.
Racing Victoria said these incidents occurred "infrequently" and insisted Victoria has one of the "best safety records in the world in racing".
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Channel 7 commentator Bruce McAvaney said it was a "tragedy" while his colleague Richard Freedman had made a point of mentioning how agitated The Cliffsofmoher looked before the race.
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But it was also noted in the coverage that the horse frequently did this before races, including when he ran without incident last start in the Caulfield Cup to finish third.
It's the first time an England-trained horse has won the Cup, with Charlie Appleby winning after several attempts. Racing Victoria vets found he was lame in the near foreleg after the race.
A year later pre-race favourite Admire Ratki died after collapsing from heart failure in the stalls minutes after the race.
Regal Monarch, trained by Chris Waller, was euthanised after falling in race four past year, while British stayer Red Cadeaux was put down two weeks after falling and breaking a leg in the 2015 Melbourne Cup.
"Internationally we have campaigned over here the last three years now and have been competitive but we have always learnt each trip what horse we felt was going to be needed on the big day".
"Unfortunately these things can happen to a horse galloping around the field at home", he said.
The horse was put down as a result of the injuries sustained.