The horse racing industry has rejected cruelty claims after two horses died in the Melbourne Cup, saying critics have no idea how well the animals are treated.

Co-owner of Melbourne Cup winner Protectionist, Jamie Lovett, said campaigners condemning racing over the deaths of Admire Rakti and Araldo did not understand the industry.

"I wish these guys would go to the track at five o'clock in the morning and see how these people care for their horses," Mr Lovett said.

"There would be no argument if you could see."

Japanese stallion Admire Rakti had been favoured to win the Cup but became distressed during Tuesday's race and died of heart failure in its stall minutes after the race.

Araldo placed seventh but was spooked by a flag in the crowd on the way back to weigh in.

The horse kicked out and broke a rear leg on a fence and had to be put down by vets.

Victorian racing officials have quickly acted to introduce measures to prevent a repeat of the incident.

After the remaining Group One races of the spring carnival, horses will come back into the mounting yard through the clock tower gate, rather than down the pathway to the mounting yard with other runners walking closely behind.

And flags will be restricted to 1m x 1m and banned from the immediate vicinity of horse movement areas with extra security in place.

The Coalition for the Protection of Racehorses called for a ban on the use of whips in racing and a ban on racing of two-year-old horses.

"We believe that pushing horses beyond their physical limits through use of the whip, and racing horses while under-developed at two years of age are significant factors as to why horses break down on the racetrack," spokesman Ward Young said.

The group said 125 horses had died on Australian racetracks in the year to July 31.

It has campaigned publicly against the racing industry, including at Monday's pre-Cup parade in Melbourne.

The group sparked complaints in October when it ran billboard posters on a Melbourne freeway of a dead racehorse to highlight the number of horses put down.

Trainer Robert Smerdon, who has three horses running in Thursday's Oaks at Flemington, said racehorse deaths were blown out of proportion by activists.

"It's such a very minimal occurrence that unfortunately happened on a big stage to the main player," he said.

Racing Victoria vet Dr Brian Stewart said an autopsy carried out on Admire Rakti had confirmed the six-year-old horse died of heart failure.

He said whipping had not contributed to the death.

Dr Stewart said a defibrillator could have saved Admire Rakti but equine defibrillators were not used because the condition was rare.

"That would have been the treatment of choice if it had been done very quickly, but defibrillators, we will review. Whether it is practical, I don't know," he said.

Governing body the Australian Racing Board said if protesters' claims of 125 deaths were correct it represented 0.07 per cent of the 189,259 horses to run in races in the 2013/14 racing season.