The Queensland woman in her 30s transited through Canberra on flight QF-1543 from Townsville on October 7, and travelled on to Melbourne.

It came as the ACT, which has surpassed three months without a new infection, returned more than 100,000 negative COVID-19 tests.

ACT deputy chief health officer Vanessa Johnston said all close contacts from the flights had been contacted and told to get tested for COVID-19 and go into quarantine.

Other passengers and anyone around Canberra Airport gates 13 and 14 between 8.30am and 10am have been told to watch for symptoms and get tested if they develop.

"The source of her infection is still unknown so Victorian, Queensland and the ACT health directorates are working together to investigate that and all three jurisdictions are contact tracing the flights she was on in that period," Dr Johnston told ABC Radio Canberra.

"We really do believe the risk of transmission to Canberrans on the flight and whilst at the airport is very low."

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Dr Johnston said the woman returned a "low-positive" result on October 10 in Melbourne and had been asymptomatic during the flights, she also wore a mask throughout her journey and "stayed well away" from others during transit in the ACT.

She said health authorities were "not concerned" about the risk of broader transmission at the airport.

"The cleaning protocols are very robust," she said.

"We're very confident with the way the Canberra Airport is managing risk mitigation protocols in relation to COVID."