The female captain was suspended following the incident last week on a Boeing 767-300 jet that had been about to take off from Sydney for the flight to Brisbane, the Australian carrier said.
“A Qantas captain was withheld from service for administrative reasons,” an airline spokesman said.
“The matter is being investigated and it would be inappropriate to comment further.”
Reports said the pilot was ordered off the plane as it started taxiing towards the runway after cabin crew alerted the flight operations manager that she may have been under the influence of alcohol.
The jet reportedly returned to the domestic terminal and a replacement pilot was found to take charge of the flight.
The Civil Aviation Safety Authority (CASA) said it had been advised of the incident by Qantas, which was dealing with the matter under its drug and alcohol management policy.
“Qantas confirmed to us that it was a positive test,” CASA spokesman Peter Gibson told AFP, adding that the pilot would remain suspended until a full investigation had been carried out.
While airlines in Australia have their own drug and alcohol management programmes, CASA also conducts random testing across the industry.
Gibson said that over the last three years 51,000 tests had been carried out with only 45 positive results.