The tests were ordered after a stallion returned a weak positive result for the virus. The horse was re-tested and returned a negative test, leading to the suspicion that the first result was a "false positive".
However, authorities were taking no chances and ordered two tests on all 74 horses held at the facility near Sydney, where the virus from last year's outbreak had escaped.
Federal Agriculture Minister Tony Burke said last night he had received advice that the first series of tests for equine influenza at the Eastern Creek Quarantine Station had returned negative results.
The Elizabeth Macarthur Agricultural Institute near Camden carried out the testing.
"As I informed Parliament, samples from the 74 horses were also sent to the Australian Animal Health Laboratory in Geelong," he said.
"I will provide a further update as soon as I receive the results of those tests."