Department of Primary Industries chief veterinary Officer Dr Ron Glanville said the 1400 horses were located on 150 individual properties in the inner red sone of south-east Queensland.
"Vaccination of the performance and pleasure horse sector was made possible when the National Management Group (NMG) allocated 26,000 doses of vaccine in late October, which were in addition to those vaccines allocated to the buffer zones and racing sectors," he said.
"At this stage, vaccination of horses is generally only approved if they are presently located in the inner red zone (the south-eastern corner of the red zone), and they are 2km or more from an active infected property. Vaccination closer than 2km will be considered if there are special circumstances that apply."
An active property is any location where clinical signs of horse flu have been confirmed in the previous 21 days.
Dr Glanville said the main purpose of vaccination was to reduce the number of horses that become infected, thereby reducing the amount of virus shed, and the chance of further spread of disease.
"The first priority of the vaccination strategy was to establish buffer zones within the red zone, as well as vaccinating those large groups of horses at racing precincts where there is significant contact with people moving between stables," he said.
"We have now reached the point where we are vaccinating other large groups of horses within the inner red zone.
"This will further reduce the chance of the illness spreading any more than it already has.
"Vaccination of horses between the buffer zones is generally not done unless the owner needs to move horses into the inner red zone for activities such as competition.
"Over the past month the rate of infection has slowed significantly, which confirms the success of our vaccination strategy and tight movement controls.
"If they have not done so already, all horse owners in the performance and pleasure sector should complete a vaccination application form and send it to their nearest participating EI vaccination accredited private veterinarian."
Meanwhile, owners of horses vaccinated against fluin the Dubbo buffer, or within the Dubbo red zone, have been advised to call the Dubbo Local Vaccination Centre if their horses have not received their second shot.
NSW deputy chief veterinary officer Ian Roth urged horse owners who have not been contacted by the centre to phone 6881-6074 to arrange an appointment.
"We are hoping to complete second round shots next Wednesday, so we would like anybody we have been unable to contact to call us by Tuesday," he said.
"The effectiveness of the EI vaccine will be limited if horses do not get their second jab, so it's vitally important horses receive both shots."
Mr Roth said about 2193 horses in the Dubbo buffer and red zone received the first shot.
"The second round is taking less time to complete as the horses have already been microchipped and tested."
"If we can clear EI from the Dubbo district, no further vaccine injections will be required."
In South Australia, agriculture authorities are expected to release guidelines within a few days for the conduct of non-racing horse events.