A massive stockpile of horse flu vaccine is available for immediate shipment to Australia from the United States, but the federal government is yet to order it, Thoroughbred Breeders Australia says.

As a war of words erupts between various racing bodies over which state should be given preference to use a French vaccine, it's been revealed federal Agriculture Minister Peter McGauran is aware of a new source of anti-flu medication.

A stockpile of 100,000 vials of equine influenza (EI) vaccine from the United States pharmaceutical company, Fort Dodge Animal Health, is available for immediate use, and could arrive in Australia by the weekend if ordered now by the federal government.

Thoroughbred Breeders Australia president John Messara said his advice from scientists was the Fort Dodge vaccine would be just as effective as the French vaccine.

"It hasn't been ordered. They (the federal government) are buying a particular vaccine, but they know the Fort Dodge vaccine also would be most effective," Mr Messara said.

"There's not just one vaccine that will work against this virus, and as a result a second vaccine is available and stockpiled in America if authorities want to buy it.

"We're talking about rolling out vaccine in small dollops because we've only got a limited amount, but we should be looking at other sources of supply of vaccine.

"The Fort Dodge vaccine is different to the one we're going to use now, but it's anti-EI, and according to scientists will work against this disease.

"If we ordered the Fort Dodge vaccine today from America, it could be here by the weekend."

Comment was being sought from the minister's office.

Mr Messara, Australia's largest breeder who runs Arrowfield stud, said he also had been advised a third vaccine was available from another overseas company.

However, he said the decision to order the US vaccine was in the hands of Mr McGauran.

"It's up to the minister. He's got all the information and we've brought it to his attention," Mr Messara said.

"I'm not a scientist but I've sent the scientific papers to him (Mr McGauran)."

A shipment of 20,000 vials of EI vaccine is due to arrive in Sydney on Thursday, but Queensland's allocation of 9,000 will not reach Brisbane until Friday, at the earliest.

Queensland faces the very real prospect of having no racing in Brisbane until February next year after EI was confirmed in two horses at Hendra, while six horses at Deagon in the state's south-east are also suspected to have EI, along with some harness horses at Albion Park.

Queensland authorities hope to begin inoculations on Saturday before a further 30,000 vials arrive from France next week ahead of another shipment of 100,000 vials.