It is understood the birds have been taken for testing by Hong Kong's Agriculture, Fisheries and Conservation Department.
Bird flu is not known to affect horses but it can jump to people. Millions of birds have been culled across Asia in recent years as authorities move to minimise the risk of the disease jumping to people.
Hong Kong's worst outbreak of bird flu was in 1997, when six people died.
The Olympic equestrian events are being held in Hong Kong because of equine disease concerns around mainland China and quarantine issues.
It is not known when the test results on the dead birds will be revealed.
Meanwhile, the 200 or so horses may end up having more than just heat to contend with as the games loom.
Hong Kong's air pollution has been officially classified in the high range recently.
The stables, however, provide a more pleasing environment, with air conditioning and a constant temperature of 23deg.