The number of infections in the purple zone is declining as equine influenza burns out.
As immunity builds up in vaccinated buffers, opportunities for the virus to spread become limited.
NSW deputy chief veterinary officer Ian Roth said new infections would mainly be confined to horses within the contained purple zone that had so far remained healthy.
"We are now targeting healthy horses in the purple zone so they can build up immunity and speed up overall recovery in the zone should they become infected," he said.
"Vaccination in the purple zone is proceeding smoothly, with 40 local veterinarians working strategically throughout the zone.
"Our teams are vaccinating around 1000 horses a day and are expected to continue at this rate if the weather stays fine."
Vaccination teams are mainly targeting isolated pockets that complex digital mapping has identified as having a combination of high horse densities and low infection rates, according to Mr Roth.
"We are conducting a targeted campaign, not blanket vaccination, and we want to remind everyone registered that they must be patient," he said.
"Veterinary teams will now vaccinate horses within 1km of an infected property, if the infection is not active."
Mr Roth said owners of uninfected horses should contact their own veterinarian to apply for vaccination. "A decision on whether to vaccinate will then be made based on the location and proximity to known new infection," he said.
Meanwhile, sample testing across various locations in NSW is continuing each day. Areas that have tested positive in last 24 hours are Grenfell, Lisarow, Armidale, Matcham, Lakesland, Pheasants Nest and Ourimbah.
All are within known infected areas and some of these properties may have already been recorded as positive. There were more than 900 properties giving negative tests.
To date, 40,559 horses in NSW have caught the flu, across 5408 properties. However, the number of cases still considered potentially active is now much lower.
In Queensland, there are 2176 infected properties. There were 29 new properties identified since Saturday - nine of them on the same road. There is a continuing reduction in infected properties due to reclassification to the status of R (resolved).
A property's R status means that its horses are no longer shedding the virus.