The woman's diagnosis has prompted health authorities to ask scores of people who may have been in contact with her to get tested.
Anyone who worked with the woman or caught the same train between Minto and Sydney and the light rail service to Darling Harbour is being asked to get tested and isolate until they hear from health authorities.
"It's sort of a hold and stay until we've assessed the extent of what is going on," Chief Health Officer Kerry Chant told reporters on Thursday.
Urgent genomic testing is underway to determine how the woman contracted the virus, with results due within 48 hours.
Authorities are concerned the woman may have been infected through another worker.
"She didn't have contact with infected overseas quarantine patients directly... so at the moment, there isn't a smoking gun in terms of how we would say the transmission event happened," she said.
The woman first experienced fatigue on Saturday and wasn't tested until Wednesday, but Dr Chant defended her.
"All of us would for non-specific symptoms take a few days to do it (get tested)... let's have some sense of reality," she said.
"We have to be very cautious in calling that into question."
Premier Gladys Berejiklian said the situation was very serious, but being managed.
This is a real test for NSW, but I'm confident if we continue the path we're on, that we will pass this test yet again.
The woman, who performed house duties at the Novotel and the Ibis at Darling Harbour, was diagnosed late on Wednesday.
Her five household members have since returned negative tests, and NSW Health is awaiting the test results of a small number of her close contacts.
As a precaution, NSW Health is also conducting wider testing of staff at the hotel complex.
Breaches of hotel quarantine are bound to happen, the premier says, with the state due to welcome back its 100,000th returned traveller in coming days.
The news comes a day after Ms Berejiklian announced a swathe of social restrictions would be eased from Monday.
There were no plans to rescind the relaxed measures at this stage.
"But it is an evolving situation and if that advice changes, then we will act accordingly," she said.
Meanwhile, NSW Health is calling on people in Sydney's northwest to get tested if they have even mild symptoms after traces of the virus were detected at a sewage treatment plant in Riverstone.
Fragments of the virus were detected in samples taken on Sunday from the sewerage system that drains parts of Riverstone, Vineyard, Marsden Park, Shanes Park, Quakers Hill, Oakville, Box Hill, The Ponds, Rouse Hill, Nelson, Schofields and Colebee.