The Australian Veterinary Association said it supported the restart of so-called "phantom" races, but warned the racing industry's problems were not over.
"This is a disaster for Australia's horse industry, and a return to betting is absolutely not an indication that the overall situation is improving," said association president Diane Sheehan.
The "phantom" races are held at one location with betting at another track via video link. Only tracks free of the virus can hold these races.
Racing got under way under biosecurity measures at tracks in Sydney and Brisbane on Saturday, but witnesses said the biosecurity measures in Brisbane were not effective and were frequently breached.
The Eagle Farm course where the races were held was divided into three "red," "yellow" and "green" zones, which people were barred from exiting unless they were leaving the course for the day.
The Australian Associated Press reported from Eagle Fram that the rules were often broken.
Sheehan said thousands of people have had their incomes drastically cut already.
Hundreds of vets in the worst-affected states of New South Wales and Queensland had had their incomes reduced by up to 90 percent.
The incomes of many horse owners had stopped altogether, but they still needed to feed stock, she said.
"These people will take a long time to find their feet again," she said. "The racing industry is undoubtedly very important, but it is only the tip of the iceberg."
Many people were in "a state of acute financial and emotional distress," she said.
The phantom races are one of a number of measures officials have thought up to try to rescue Australia's multi-billion dollar racing industry.
Horse movement is at a standstill in the states of New South Wales and Queensland. Officials have ordered an inquiry into how the disease got into Australia.
Attention so far has focused on a government quarantine centre on Sydney's western outskirts.
Equine influenza is a highly contagious virus that is harmless to humans but causes respiratory problems, fever and sometimes death in horses.