Authorities do not believe the outbreak has peaked yet, with more than 3000 horses in New South Wales and Queensland that are known to have been exposed to the virus under surveillance. However, positive results in recent days have nearly all been among the so-called "suspect" population.
The ban on horse movements remains in place across New South Wales and Queensland.
Authorities in both states are investigating alleged breaches of the movement ban.
The NSW Police Force Rural Crime Unit is exploring two cases. In one case, a horse was found among a semi-trailer load of cattle which was pulled over by a routine police patrol. The other case involved a tip-off.
"The standstill is designed to help horse owners by stopping the spread of horse flu," said Ian Roth, the deputy chief veterinarian with NSW's Department of Primary Industries.
"To get on top of this disease and stop its spread, we need people to be vigilant about keeping their horses at home. People who are moving horses in NSW are breaking the law and risk a $44,000 fine and 12 months in jail.
"Illegal horse movements risk extending the duration and spread of the outbreak - and that would worsen the impact on people in the horse industries.
"The simple fact is you'd have to have rocks in your head to even contemplate moving horses under the current situation. Those who flout the law are letting the whole horse industry down, from pony clubbers all the way through to the racing scene."
Meanwhile, Roth confirmed a horse on a property west of Wauchope on the NSW mid-north coast had tested positive for the disease. A restricted area has been placed around the property.
The horse had attended an event held at Narrabri on August 31, and was already in quarantine based on its link to that event.
There are now 17 restricted areas across New South Wales.
The state's far north coast remains free of equine flu after a a negative test result from a property near Tweed Heads. "This is good news for the far north coast," said Roth, "but it doesn't mean horse owners can become complacent."
Negative test results for equine influenza have now come back from five locations on the far north coast. Samples from horses near Casino, Lismore, Grafton, Tweed Heads and Yamba have returned negative tests.
However, not all the news has been good. The discovery of the virus in the breeding heartland of the upper Hunter Valley is a further blow to the already crippled thoroughbred racing industry.
The disease was detected in broodmares on a stud farm.
Breeding districts are in particular danger, as the disease can kill up to 40 per cent of the foals it infects. Hunter Valley studs are the nursery for around 40 per cent of Australia's thoroughbred foals.
To date, the virus has been detected on just the one stud farm.
While plans are afoot for "phantom" race meetings in some venues, racing in NSW is effectively at a standstill. Randwick Racecourse, home to about 700 racehorses, is under lockdown. Up to 90 per cent of the animals housed there are now said to be showing signs of the flu.
In other news:
Minister for Primary Industries and Fisheries Tim Mulherin said this was a small, but important step on the long path towards recovery from Equine Influenza.
"While the threat from Equine Influenza continues, we must continue to have very tough restrictions on horse movements and enforce those restrictions," Mr Mulherin said.
"But it will now be possible for some horse events to be held under strict conditions and with the approval of the chief inspector of stock.The chief inspector of stock will need to be fully convinced that there are sufficient controls in place to prevent the spread of equine influenza."
The movement of horses without a permit is still illegal in Queensland. Approved horse events will only feature horses that are already in the event precinct as they cannot be transported.
There is still a ban on horses crossing state borders, Mr Mulherin said.