A second shipment of equine influenza (EI) vaccine has been expedited and will arrive in Sydney on Friday.

The original arrival date was set for October 9 but authorities worked to speed up the delivery of the 130,000 vials of the vaccine to ensure there would not be a repeat of Friday's frustration when it took 10 hours longer than expected to get the inoculations underway.

Of the 20,000 vials in the initial delivery, 4,000 have been given to racehorses in training in risk areas of NSW as well as horses on agistment farms.

Queensland's vaccination program is also underway while Victoria is expected to begin vaccinations on Monday.

So far, NSW and Queensland are the only two states to be affected by the highly contagious disease with EI-free Victoria to inoculate horses engaged in the spring carnival as a priority.

"The next shipment of 130,000 will arrive at 6am on Friday," Racing NSW chief executive Peter V'Landy's said.

"We want to do a lot more horses.

"How many NSW will get hasn't been determined but we will be asking for as many as we can get."

Racing NSW stewards and dozens of veterinarians spent 10 hours waiting to take delivery of the vaccine on Friday while biosecurity protocols and bar-coding of the genetically modified substance were undertaken.

Chief steward Ray Murrihy said the delay could have been serious.

"We were trying to get the vaccine to the horses at Rosehill and the provincial tracks as soon as possible and it was frustrating," Murrihy said.

Rosehill is the only one of three training facilities in Sydney that doesn't have the virus, with stables at Randwick and Warwick Farm in quarantine.

All horses at Rosehill as well as Kembla Grange south of Sydney and Gosford, Wyong and Newcastle to the north, have now had their initial shots.

There will still be an anxious wait with full immunity against EI not guaranteed until some time after the horses receive a booster shot in two weeks.

The teams of stewards and vets moved to spelling farms on Sunday to try to protect the horses who will come into work later this year and form the bulk of the summer and early autumn carnivals.

Racing in Brisbane came to a halt last week when EI was confirmed in metropolitan stables at Hendra.

However, it is hoped 250 equestrian horses and their carers who have been stranded at Morgan Park in south east Queensland for more than a month will be allowed to leave later this week.

Initial vaccination of racehorses at the Gold Coast has also been completed over the weekend.

New Zealand authorities have cleared Brisbane trainer Robbie Heathcote after a frantic search for him in Auckland on Saturday after he admitted deliberately infecting his horses to speed up the inevitable process after horses at a neighbouring stable were confirmed with EI.

Heathcote arrived in New Zealand for a holiday on Friday but has since satisfied MAF Biosecurity officials there that he followed all protocols including purchasing new clothes and suitcases before heading across the Tasman.

An independent inquiry headed by retired high court judge Ian Callinan into how EI infiltrated Australia will get underway in Sydney on Wednesday.

The first case was confirmed on August 23 in a stallion awaiting release from the Eastern Creek quarantine station after he travelled from the northern hemisphere.

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