Problems with the whip were a “perception problem” because the whip was padded and the way it was allowed to be used had changed, he said.
“The one thing that will remain is that the whip is necessary for safety for the jockey on top to control the horse when safety becomes an issue,” Thompson told the ABC on Monday.
“Ultimately it will go, I think the community will demand it goes and I think basically we’ll have it go but it will stay for safety reasons.”
“It will go for encouragement reasons at some point in the future.”
Thompson said Racing Victoria was already using the betting money that fills its coffers to fund horse welfare programs.
“Those funds are coming from both the Racing Victoria coffers and also as deductions from prize money,” he said.
He said the one per cent levy on prize money would double to two per cent next year.
Thompson pointed to a program launched last week that would focus on the horse breeding industry.
The horse racing industry has been under fire since an ABC 7:30 report in last month which revealed hundreds of racing horses were being abused before they were sent to the slaughterhouse.
There have been calls by some groups for a royal commission into the industry.
Thompson said some would have been shocked by the report but he said the industry was “tackling the challenges”.
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