However, Rachel Stephen-Smith has clarified if a person is required to provide a certificate of a negative result, that person will be invoiced for the certificate after the test is undertaken.

Ms Stephen-Smith said the territory changed its advice on Tuesday night after federal Health Minister Greg Hunt clarified free testing for domestic travel was covered by an agreement between the Commonwealth and state and territory governments.

"This testing will now be offered to individuals free of charge at all ACT government testing centres," she said.

"The details of the funding arrangements are still to be clarified."

This comes after a number of people were forced to pay $112 for a COVID-19 test when they were not required to. This was in part due to confusion around whether jurisdictions required a certificate to prove a negative test. Queensland sought to clarify this week that a text message with a negative test result would be enough proof.

Ms Stephen-Smith said the government would seek to refund those who had been incorrectly charged for their COVID-19 test, she said did not know the exact number of people but indicated it was a small number.

The ACT's opposition has accused the government of breaching the National Partnership on the COVID-19 Response for the tests.

"The COVID-19 health response is very clear. It says if somebody has to have a COVID test that it will be free," opposition health spokeswoman Giulia Jones said.

"If they are required by government to have a test, they will not be charged, that is the agreement. I don't know understand why Canberrans have been charged $112 for tests in the ACT when they are required by state and territory government regulations."

Ms Stephen-Smith said it had been "a really confusing 48 hours", after she had initially set out on Tuesday that government facilities would not undertake tests where people were required to pay.

She later said the government facilities would charge for tests in certain circumstances, including when people needed a negative result to travel, prior to her comments on Wednesday morning.

Ms Stephen-Smith said the conflicting advice had been driven by confusion over whether other jurisdictions required a certificate to prove a negative test or if a text message would be enough.

"In practice testing centres that have been run by Canberra Health Services have often tested people with no charge when they did not require a certificate but for those people who did require a certification, they were advised that they would be invoiced for that," she said.

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Ms Stephen-Smith accused Mr Hunt of changing his advice. She said earlier on Tuesday the federal Health Minister said that asymptomatic testing should not be required for interstate travel.

She accused Mr Hunt of backtracking on this on Tuesday evening, when he said the Commonwealth had always funded PCR testing on a 50-50 basis with the states and territories, regardless of the reason for the test.

The National Partnership on the COVID-19 Response does set out the payment agreement between the Commonwealth and state and territories on testing arrangements and it has always been the case the cost is shared.

But the certificate is not included as part of this. Earlier in the week, Mr Hunt wrote to Queensland Health Minister Yvette D'Ath saying that large scale asymptomatic testing was strongly discouraged. He has advocated for rapid antigen tests.

However, Mr Hunt confirmed that tests had always been covered by the agreement and his advice had never changed.

"We've been covering these tests on a joint basis since the Queensland Premier, on March the 13th last year in 2020, signed the shared funding agreement with the Commonwealth," Mr Hunt told 4BC Breakfast.

"What does it mean for the public? Tests have been covered as they always have been. The Commonwealth has paid half throughout."

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