The new zoning in NSW, to be introduced tomorrow, will see restrictions on horse movements softened in some areas, particularly the important breeding areas of the Hawkesbury and the Hunter.
The announcement came as the number of infected properties hit 1363, home to 11,872 horses. Another 670 properties are considered suspect.
Infected properties are all within containment lines.
The special purple zone is designed to allow breeding activity to be conducted in key areas. It allows horses with a permit to be brought in for breeding purposes, but they cannot leave until authorised by agricultural staff.
Macdonald said the four colour zones were introduced based on information gathered by epidemiologists, surveillance teams and field veterinarians.
The zones are:
"The challenge now is to let horse owners know where they fit within the equine flu protection plan and ensure they fulfil their responsibilities.
"It is clear zoning hinges on the support of the general public and, importantly, each and every horse owner - no matter whether they own a racehorse worth tens of thousands or a companion pony.
"The value of these horses to their owners is the same - the government recognises that.
"We are doing all we can to eradicate this problem."
In Queensland, a new green zone was introduced today, which eases restrictions.
However, full movement restrictions are still in place in the existing red zone and owners must apply to the Department of Primary Industries for a licence/permit to move a horse. Moving a horse includes riding or leading it outside its property.
Horses cannot be moved between zones without a permit.
Meanwhile, South Australia has introduced a permit system for bringing horses into the state.
People wanting to bring horses in from Victoria, Western Australia, Northern Territory or Tasmania may be able to get permits for travel, but horses from New South Wales and Queensland remain banned.
South Australia's Chief Veterinary Officer Dr Rob Rahaley said that this was an important step in recovering from the horse flu outbreak and would help those people whose equestrian business activities involved regular border crossings.
"I am keenly aware that many people along the South Australian/Victorian border have suffered due to the movement restrictions put in place to ensure that SA remains free of horse flu," he said.
"Victoria has stepped up security at its NSW border and, like South Australia, is free of horse flu. So, given that situation, I believe allowing movements under permit is a manageable risk but we remain on high alert."
Dr Rahaley said people in South Australia wanting to move horses would need to apply for a permit and obtain a veterinary certificate validating the health of the animal.
"Horses staying longer than 24 hours in Victoria will also need a new health certificate to return under permit to South Australia.
"Horses returning within 24 hours (travelling to and from single events, such as race meetings) will not need another health certificate."
Dr Rahaley said that he was pleased with the way SA horse owners had complied with the movement bans and in cancelling their events.
"Cancelling events and restricting movements has been difficult but it has been necessary to do this - if horse flu was found in this state the impacts would be devastating and would last for many months," he said.