The Aidan O'Brien-trained horse suffered a fractured shoulder during Tuesday's race and had to be euthanised, Racing Victoria's executive general manager of integrity services, Jamie Stier, said in a statement.
Mr O'Brien said: "Unfortunately these things can happen to a horse galloping around the field at home".
Jockeys were guided away from The Cliffsofmoher as vets arrived on the scene at Flemington.
The condition of The CliffsofMoher, which was being ridden by star English jockey Ryan Moore, is not yet known.
Cross Counter was the final victor of the Melbourne Cup after a nail-biting final, taking the lead in the very last seconds of the home stretch.
"It's very sad. It could have been worse, Ryan [Moore] could have taken a fall off him, someone could have been seriously injured". "He's really sweating up badly", horseracing commentator and Sports Sunday panellist Richard Freedman said before the race. Meanwhile, second and third place went to Marmelo and A Prince Of Arran.
Sam Ballard: Sydney man who swallowed slug passes away
In 2016, Katie Ballard applied to the National Disability Insurance Scheme (NDIS) when Sam became eligible for a £300,000 package. As a result of the parasite, Ballard contracted a type of meningitis tied to rat lungworm , and things went downhill from there.
The race is held over a distance of 3200 metres, the traditional two-mile cup distance, for horses three years and older and is the richest and most prestigious two-mile handicap in the world.
Viewers were left devastated by the news of the horse's death after the race.
In 2015 Red Cadeaux, a British Thoroughbred who had finished runner up in 2011, 2013 and 2014, was euthanised following complications in surgery for an injury sustained in the race.
The Melbourne Cup has again been marred by the death of a horse, this time the Irish-trained The Cliffsofmoher.
Araldo placed seventh but was spooked by a flag in the crowd on the way back to weigh in, kicking out and breaking a rear leg on a fence.
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