This week's arrival of vaccine against equine influenza (EI) may come too late for the Australian racing industry as the virus continues its rampage through NSW and Queensland.

The first 20,000 of 150,000 vials of the vaccine are due in Australia from France on Thursday with the priority being racehorses and high level equestrian performers.

But with the news that racehorses trained at Doomben in the Brisbane metropolitan area are suspected of having the virus and a further scare at Kembla Grange south of Sydney, the outlook is not as hopeful on Monday as it was on Sunday.

Rosehill remains the only one of the three Sydney training centres still free of EI and horses are due to be vaccinated there on Friday morning.

But Chris Waller said he and his fellow trainers faced a nervous few days.

"It's probably only a week away from Rosehill," Waller said.

"There is the odd pleasure horse or kid's pony in a backyard probably every two or three kilometres, enough for EI to find its way to Rosehill.

"We'll hopefully get to Friday, get it (vaccination) out of the way, then wait a week and maybe then we can breath a bit easier."

Warwick Farm is currently shut down after EI was confirmed at the outer Sydney track on Saturday morning, a month after EI infiltrated stables at Randwick Racecourse in the eastern suburbs.

Racing in Sydney is unlikely to resume until the new year with the autumn carnival now expected to be put back a month.

Queensland Racing Limited (QRL) chief operations manager Malcolm Tuttle said Brisbane was now looking at the same scenario.

"Racing is worth $110 million in wagering alone in Queensland and it contributes more than $700 million to the Queensland economy," he said.

"This is the worst possible news for racing in Queensland.

"At this stage it looks like we'll be out of action for at least October and November in Brisbane and that means the Magic Millions at the Gold Coast is now in serious doubt of being held, even if it's a February date."

However, hopes are still high that Victoria will remain free of EI and the rich Melbourne spring carnival will continue.

Federal Agriculture Minister Peter McGauran said he was still worried about the fate of this year's Melbourne Cup carnival, but he believed vaccinating horses would help secure the event.

"I believe the Melbourne Cup will proceed, but there is a nervous wait for three weeks until the immunity is acquired by the Cup runners, who will be vaccinated towards the end of this week," McGauran told reporters.

"Nobody should relax, let alone celebrate, until the horses pass the finishing post.

"Nonetheless, everything possible is being done and the vaccination of the spring carnival horses is an added insurance."

NSW and Queensland will receive the bulk of the first shipment of vaccinations with around 1,500 going to Victoria for the horses targeting the spring races.

Although Racing Victoria said the number was inadequate, McGauran said it was what the Victorian government had requested.

Both McGauran and NSW Primary Industries Minister Ian Macdonald have defended the delay in acquiring the vaccine saying it was not possible to order it until the exact strain of the virus was determined.

Racing NSW chief executive Peter V'Landys described Sunday's announcement of the forthcoming vaccine as a breakthrough but said he was still cautious.

"Hopefully, this is the big breakthrough we have been looking for," V'Landys said.

"This is a floodlight at the end of the tunnel but up until this stage the equine influenza train keeps running us over."

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