Racing Victoria is disappointed by the new strict rules and have appealed for them to be changed but Racing NSW said the measures would come into effect immediately with no end date set.
A Racing Victoria spokesman encouraged a "review of these new protocols in consultation with the approved horse transport companies and industry stakeholders at the earliest opportunity", they told Racing.com.
"We think this is an unnecessary burden placed on owners and trainers in both states given that horses are not carriers of Covid-19.
"Since March, a group of industry-approved horse transport companies have been floating horses between the two states under strict biosecurity protocols without issue.
"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."
But Racing NSW chief steward Mark Van Gestel said the decision to ban horses from Victoria was immediate and also affected NSW horses returning home.
"We've put the protocols in place on the basis of risk assessment," Van Gestel said.
There are few New Zealand-trained horses racing in either state and the few in Victoria are mainly jumpers or horses who would have little reason to head north of the border during winter.
But movement between the two states will become increasingly important in a month.
August is when the early season major races start to roll out and then into September and beyond the ability to move between states is crucial for horses seeking the right races, often ruled by track conditions or chasing black type.
The two highest profile New Zealand gallopers in Australia are Melody Belle and Probabeel, both in New South Wales but with potential Victorian targets in the spring.
If any bans on horses continue for months it would have a catastrophic effect on the famed Victorian spring carnival, home of the Melbourne Cup.
That carnival is already facing having no Japanese superstars this spring as well as far fewer European raiders.