ACT Health reported two men returned weak positive results for COVID-19 on Wednesday.

Health Minister Rachel Stephen-Smith confirmed on Thursday both those cases were new infections, rather than historical infections.

She said they both tested negative before travelling to Singapore to take a repatriation flight to Canberra this week.

She said it was therefore "likely but not definite" they acquired the infection in transit.

ACT chief health officer Kerryn Coleman said contract tracing of a "very small group" of close contacts was underway.

She said the two men, one in his 40s and a teenager, were moved to a separate area of the hotel and their symptoms were being closely monitored.

All other hotel guests returned negative tests on the first day in quarantine and Dr Coleman said they would all be tested again in coming days.

"We're looking at that being done around day five or six ... that's the next point of risk we would expect to see symptoms and infection," she said.

Dr Coleman said Canberra's hotel quarantine system was "really robust" and made assurances the ACT had learnt from other jurisidictions.

She said all hotel quarantine staff have daily symptom screening and regular COVID-19 testing, including daily saliva tests.

Dr Coleman said health authorities were also communicating with NSW Health and Singapore Airlines about the cases.

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ACT Health said the individuals were not known to have met with anyone who was unwell or with COVID-19 in the days before travelling.

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