The action to cancel Thursday's races was taken with unanimous support of the BHA's industry veterinary committee and will affect meetings at Huntingdon, Doncaster, Ffos Las and Chelmsford.
Donald McCain's yard was the only one represented at both tracks.
As a result, any trainer who ran a horse at those meetings has had restrictions placed on their movement.
Racing woke up to the news that all four scheduled race meetings in Britain on Thursday have been cancelled following confirmation of three cases of equine flu in vaccinated horses in a racing yard which sent runners to the meetings at Ayr and Ludlow on Thursday.
The British Horseracing Authority reported horses from the infected yard raced at Ludlow and Ayr on Wednesday, adding identification of the virus in vaccinated animals presented a "cause for significant concern".
Equine influenza is a highly infectious disease of horses, mules and donkeys occurring globally caused by strains of Influenza A virus.
In a statement, he said: "Bankhouse (his stables) follows all the available advice on disease control and all our horses are fully inoculated".
No further positive tests have been recorded, but another three days are needed before it will be possible to make a decision on whether it is safe to resume racing as the disease can take that long to show its symptoms.
Horse racing in Britain has been cancelled until at least Wednesday over an outbreak of equine flu.
The governing body's statement added: "The BHA is presently communicating with yards potentially exposed to ensure appropriate quarantine and biosecurity measures are put in place and horse movements restricted to avoid possible further spread of the disease".
The BHA said the full extent of the problem was not yet known but it has worked quickly to identify which yards could have potentially been exposed.
So what exactly is equine influenza, and why has it got so many people in the horse racing industry so anxious?
The Animal Health Trust are working alongside the racing industry on the matter and a further update is expected later on Thursday.