The decision has been made by the British Horseracing Authority after three vaccinated horses in an active yard were tested positive for the disease on Wednesday.
Leading Welsh horse trainer, Tim Vaughan, says the equine flu outbreak, which has forced the cancellation of all race meetings across the United Kingdom, could last up to 10 weeks, and could affect the Cheltenham Festival.
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.
Horses that have contracted equine flu can develop a high fever, coughing, nasal discharge and sometimes swelling of the lymph nodes.
It is the most potentially damaging of the respiratory viruses that occur in United Kingdom equines and disease symptoms in non-immune animals include high fever, coughing and nasal discharge.
But it added that "at least three more days are required before it will be possible to make a decision about whether it is safe to resume racing".
A further update on the possible continued extent of disruption is expected from the BHA - with a packed weekend of Cheltenham trials and other big races scheduled at Newbury, Warwick, Musselburgh and in Ireland.
McCain, who saddled Ballabriggs to win the Grand National in 2011 and has more than 100 horses in his stable, said "the BHA were contacted immediately" once the positive result for equine influenza had been confirmed and that he is "liaising closely with them about biosecurity and management of all the horses at Bankhouse".
The disease is however being reported in vaccinated horses.
He went on: "When new horses arrive at our yard we, as much as possible, try to keep them separate but at this stage can not know if the infection came from recent arrivals or from horses returning from racing".
Racing will continue in Ireland at Dundalk on Friday, Naas on Saturday and Punchestown on Sunday, but no English horses will be allowed to run in Ireland.
A number of stables, including those of Nicky Henderson and Paul Nicholls, were placed on lockdown while further testing was undertaken on horses who might have come into contact with the McCain runners earlier in the week.
In a statement, the BHA said: "This precautionary approach is meant to ensure we put the health of the horse population and control of the virus first, and avoid any unnecessary risk that might come from returning to racing too quickly".