In a statement, the BHA reported horses from the infected yard raced on Wednesday at Ayr and Ludlow, adding identification of the virus in vaccinated animals presented a "cause for significant concern".
The loss of Musselburgh's richest ever jumps meeting on Sunday because of a UK-wide alert about an equine flu outbreak is "a real, real shame", the clerk of the course has said. You will have to test all the other yards that had runners at Ayr and Ludlow.
Its effects are still unknown and that's what makes the stance taken by Horse Racing Ireland (HRI) and the Irish Horseracing Regulatory Board (IHRB) to continue racing as normal all the more surprising.
All racing in the United Kingdom has been suspended until next Wednesday at the earliest. However, the BHA admitted on Friday that the large number of tests now required means that the results of all its tests will not be known by the end of the weekend, when the Authority needs to decide whether there is a need to extend the current shutdown of British racing beyond next Wednesday.
In 2001 the meeting was cancelled due to the foot and mouth crisis, but with over a month until this year's meeting there is hope a similar situation can be avoided.
There were four meetings scheduled in the United Kingdom on Thursday at Chelmsford City, Doncaster, Ffos Las and Huntingdon along with Thurles in Ireland.
France is the root of this equine influenza outbreak with several sport horses in northern France testing positive for the infection.
Equine influenza is a highly infectious disease of horses, mules and donkeys.
In a statement, the BHA said: "This approach will allow samples to be collected and assessed by the Animal Health Trust in order that a fully informed decision can be made on Monday".
The outbreak was discussed in parliament on Thursday.
While all British racehorses are vaccinated against equine influenza, this strain has affected vaccinated horses. The BHA consulted with its veterinary committee before making this decision.
Speaking to BBC Scotland, she added: "I'm disappointed for the people who were coming to see these wonderful horses and who might not get a chance to see them at Cheltenham or just on TV".
The Jockey Club Estate's schooling grounds in Lambourn have been closed to outside horses as a precaution, a move which was reciprocated for Newmarket's gallops.