Racing NSW has banned horses travelling from Victoria competing in races in the northern state for an indefinite period.
However, Racing Victoria says the ban is unnecessary given horses are not carriers of COVID-19.
The Racing NSW ban comes after Melbourne and the Mitchell Shire faces a six-week lockdown due to the spike of coronavirus cases in Victoria.
Racing NSW chief steward Marc Van Gestel said the decision to ban horses from Victoria was immediate.
"We've put the protocols in place on the basis of risk assessment," Van Gestel told RSN927.
"The transport drivers required to take those horses across the border and then parking at stables, licensed premises and racecourses, Racing NSW has seen that as a risk that under the circumstances it was not prepared to take."
Van Gestel said Racing NSW would monitor the number of COVID-19 cases in Victoria, but noted as there was a six-week lockdown in place he expects the restriction on Victorian horses to remain for that period.
The training partnership of Ciaron Maher and David Eustace along with Chris Waller and Team Hawkes are a number of stables that have large operations in both Victoria and NSW.
RV argued the ban places an unnecessary burden on owners and trainers in both states.
"Since March, a group of industry-approved horse transport companies have been floating horses between the two states under strict biosecurity protocols without issue," a RV spokesman said.
"We know that the approved horse transport companies take their responsibility to owners, trainers and the broader racing industry very seriously and thus are diligent in their sanitation and handling processes.
"These are professional operators and we're satisfied with the manner in which they have managed any risks over the past four months and have confidence that they can and will continue to do so."
RV is calling on Racing NSW to review the new protocols in consultation with the approved horse transport companies and industry stakeholders.
"In the knowledge that these horse transport companies are being approved to continue their interstate operations by government, the transport of horses into Victoria by them is permitted to continue at this time under the approved industry protocols," the spokesman said.