Authorities were placed on alert when an imported horse at the facility returned a "weak positive" test, followed by a negative test.
Agriculture officials were taking no chances and ordered a complete set of tests on all 74 horses housed there, with a full set of samples sent to separate laboratories for anaysis.
The first set of results early yesterday proved negative and last night federal Agriculture Minister Tony Burke confirmed the second set returned the same result.
The negative results included those for the horse that initially returned the positive test.
Mr Burke welcomed the news.
"All the tests for equine influenza at the quarantine station have now concluded and the advice is that all horses from Eastern Creek are free of equine influenza," he said.
"While those involved in quarantine must always remain vigilant, those who love the races can now get on with enjoying the Spring Racing Carnival.
"Since the horse flu outbreak last year we made it clear we require close monitoring and strict enforcement of quarantine procedures - and that is unchanged."
The scare at Eastern Creek, where the virus originally escaped during last year's outbreak, came as horse industry leaders met in Sydney on Thursday to discuss ongoing strategies to handle any future incursions of the highly contagious disease.
The biggest issue was always going to be vaccination, with racing interests pushing for an ongoing vaccination programme for racehorses, while the Australian Veterinary Association and the Australian Horse Industry Council have opposed it.
The cost of a vaccination programme for racehorses - the cost of which the industry says it will meet - has been put at $A10 million to $A15 million.
Those at the forum heard from experts on vaccination,including two from overseas - Dr David Powell from the Maxwell H Gluck Equine Research Centre in the United States and Professor Ann Cullinane who currently heads the Virology Unit at the Irish Equine Centre.
Dr Ann McDonald, who is national manager of Australian quarantine services, spoke of recent changes in the management of equine quarantine, as recommended by the Callinan inquiry.
It was hoped the summit would result in a high-level working group to further consider the options discussed during the day.
"The working group will need to include a cross-section of government and industry, vets and others to ensure it gets the whole picture and is completely informed," New South Wales Primary Industries Minister Ian Macdonald said before the summit.
"It is particularly important that this group consider the pros and cons of vaccination in the future, including economic impacts.
"I expect that this group will report back to Primary Industries Ministerial Council by March next year."