NSW's virus-free streak has come to an end after a quarantine worker tested positive to Covid-19 after working across two Sydney hotels, one of which housed returned travellers.

The woman worked at the Novotel and Ibis hotels in Darling Harbour, with staff now on high alert.

NSW Health Minister Brad Hazzard said she carried out domestic duties at the hotels and would travel to work from Minto, in Sydney's southwest, by train and light rail.

Five family members, who the woman lives with, have so far tested negative to Covid-19 but will complete 14 days' isolation.

It is too early to tell how she caught the virus and whether or not it was from a returned traveller.

Hazzard told Sunrise he was alerted to the new case in the early hours of Thursday morning.

"We would have been saying today is 26 days without any cases, but we now have one case," he said.

Hazzard said he woke up chief health officer Dr Kerry Chant this morning to talk about the case.

"We are working through the issues," he said.

Health authorities are now racing to alert close contacts and investigations are under way.

The woman worked at the Ibis on Friday, November 27, and the Novotel – which is one of the city's quarantine hotels – on November 28, 29 and 30.

Anyone who worked at those two hotels on those days has been told to monitor for symptoms and self-isolate until they are tested and receive a negative result.

News of the case came just hours after NSW Premier Gladys Berejiklian revealed the latest wave of eased restrictions, particularly around venues and stadiums.

Hazzard confirmed the new case would not influence those changes.

When asked whether Thursday's case would trigger any change to restrictions, he said: "I doubt it very much.

"We have a fantastic public health team that manages these things extremely well.

"We are in the middle of a worldwide pandemic."

He acknowledged when the government revealed changes to restrictions, Berejiklian was transparent in the fact she expected more cases to pop up.

"As Health Minister, I anticipate that because we are in a pandemic," Hazzard said.

"If you've got any symptoms, no matter how mild, please don't go to work, please don't go shopping and stay home and wait for test results."

NSW Health released a statement that said it was conducting wider testing of hotel staff.

"The person, who lives in southwestern Sydney, travelled from Minto to Central and on the light rail from Central to Darling Harbour on a number of occasions while potentially infectious," the department said in a statement.

"NSW Health will be asking people who travelled on the same services to get tested immediately and self-isolate, until further advised by NSW Health. The route and line details will be provided later today."

The new case comes a day after Chant told reporters the virus was "virtually eliminated" in NSW.

"I think that on the balance of probability, we probably have virtually eliminated community transmission," Chant said.

"There's always room for doubt there because the virus can be so stealthy … There are no absolutes with Covid.

"But all our intelligence would suggest it's been long enough [since] having a locally acquired case where we don't know the source."

Chant did, however, caution that new cases were likely to pop up.

Twelve Sydney suburbs were put on alert on Wednesday night after traces of the virus were found in the sewage system.

Fragments of the virus that causes Covid-19 were detected in samples taken on November 29 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.

Meanwhile, just last week, Queensland Premier Annastacia Palaszczuk said the state would move to a "hot spot" system and there would have to be a "massive outbreak" for them to slam the border shut again.

"There are so many variables here, each particular case has got to be looked at on its merits and [we have to] work out what the risk is to Queensland."

The revelation also comes after West Australian Premier Mark McGowan revealed the state would open its border to NSW on December 8. This is now likely to be at risk, given NSW needed to go 28 days without a case to trigger the reopening.