Federal Agriculture Minister Peter McGauran said the programme was to have ended on November 17, but will now run an extra 12 weeks.
The money is on top of the $A110 million pledged when the assistance programme was launched.
The minister said the extension recognised continuing restrictions to contain and eradicate equine flu.
"The funding available to eligible non-government, not-for-profit equestrian organisations has also been increased.
"Those organisations that have been granted assistance already may be eligible for additional assistance, where they continue to incur costs as a result of the continued restrictions on horse movements," he said.
Weekend news of the extra funding came as the number of infected properties in New South Wales approached 5000.
The number now stands at 4919, with 451 labelled "dangerous contact" and 476 officially "suspect".
Authorities say a total of 6731 horses out of 13,476 have been vaccinated in buffer areas so far.
Surveillance testing is currently being carried out at Coonamble, Coonabarabran, Berry, Walcha and Gloucester Tops. Negative results from this campaign will allow the status for the existing red zones to be modified.
Authorities are also focusing their attention in the Barmedman and Temora areas of NSW, where tracing and surveillance has unearthed additional infected properties.
NSW Chief Veterinary Officer Bruce Christie said early action to declare a red restricted area around Temora has paid off following the detection of EI in two horses on one property at Temora and five horses on another. None are currently infectious.
"NSW DPI tracing from the infected area at Barmedman and widespread testing of horses has confirmed the two infected properties at Temora and three new infected properties at Barmedman," Mr Christie said.
"More than 200 horses around Temora have been tested in recent days and only two properties have come back positive. The strategic testing of more than 200 horses in the area gives NSW DPI epidemiologists reason to believe the disease is not widespread."
There are now four infected properties at Barmedman, one at Gidginbung and two at Temora.
The additional infected properties at Barmedman are all within close proximity of the original outbreak there, meaning there is no change to zoning in the area."
Mr Christie said a red zone had been established around Temora, Gidginbung and Barmedman a week ago and the Cootamundra and Junee local government areas had been changed from the green zone into the amber zone at that time also. No further zoning changes have been made in the area.
Tracing and surveillance teams are working to identify how the disease found its way to the Temora property and any possible spread from the infected properties.
Vaccination is already under way around the Temora area with more than 500 horses inoculated.
Meanwhile, the first horses, ponies and donkeys in the Scone and Merriwa vaccination buffers yesterday received their initial equine flu shots as part of the eradication plan.
NSW deputy chief veterinary officer Ian Roth said four veterinary teams from the Scone Local Vaccination Centre were to vaccinate 60 horses and donkeys yesterday, with the number increasing to a target of 100 per day for the rest of the week.
"The Merriwa LVC teams are vaccinating about 120 horses per day in a buffer area which runs north and south of Merriwa with the river on the western boundary," he said.
"Along with the buffer area to the east of Scone, which connects with the Gloucester buffer, we aim to contain the spread of EI in the upper-Hunter area."
The first round of vaccinations in the Scone and Merriwa buffers is due to be completed by October 26.
He stressed the need for onging good hygiene and urged horse owners to keep other people away from their animals unless absolutely necessary.
In other news, racing will return to Royal Randwick racecourse on December 1. It was the first course forced to lockdown as the virus spread.