However, authorities have given the all-clear after final results from nasal swabs and blood tests taken from 74 horses at Eastern Creek were negative.
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," Agriculture Minister Tony Burke said in a statement issued on Friday night.
The final test was on blood samples taken from all the horses, including the horse which provided a positive result for EI on its fifth mandatory quarantine nasal swab, Burke said.
"Each horse ended up being tested a total of 14 times," Burke told Sky News.
"And what it looks like is there was one rogue result that was a false positive. But certainly every one of the 74 horses has now been given a clean bill of health."
He said inaccurate positive results occurred from time to time, adding the lock-down procedure adopted over the past two days was the correct response and could have averted potential disaster.
"It's something that can happen from time to time," Mr Burke said of the rogue test.
"The way the testing's done isn't a yes/no test. It's on a scale of numbers and depending on where you land on that scale determines whether the vets consider it a positive or a negative result.
"This was only just into positive territory for EI."
In August last year, there were devastating effects when EI escaped from Eastern Creek and infected the general horse populations of NSW and Queensland.
The multi-million-dollar racing industry was shut down in both states for three months and unprecedented restrictions were imposed on horse movements.
Authorities estimate the cost of the EI breakout was some $1 billion.