The announcement came alongside reports a man from a Sydney COVID-19 hotspot entered Queensland via the ACT.

Mr Barr said there was no forewarning of the decision which would come into effect from 1am Saturday.

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He said he wasn't aware of people using Canberra to flout lockdown rules but was open to addressing the issue.

"The ACT has had no active cases for most of this week now, and no new cases for the best part of three weeks," Mr Barr said.

"All of that said ... this is our new reality.

"The hotspots are going to move around states and territories, cities and towns for the foreseeable future.

"Ultimately we have to all accept the fact we are living with this ... possible for many years into the future.

Mr Barr said it was "a fact of life" that most jurisdictions were treating the ACT and NSW the same, despite Canberra's low case numbers.

Queensland Premier Annastacia Palaszczuk announced on Wednesday the state borders would close to NSW and the ACT from 1am Saturday as both jurisdictions have been declared hotspots.

Queenslanders returning from the ACT or NSW will have to pay for 14-days mandatory hotel quarantine.

"There have been a large number of active cases in Victoria, and we are continuing to see cases in NSW. This is a very concerning situation," Ms Palaszczuk said.

"We cannot risk a second wave. We have to act decisively and today we have acted quickly. We have put Queenslanders first."

Ms Palaszczuk said the ACT had to be included in the closure after a NSW resident travelled via Canberra to Queensland, "putting everything we have in Queensland at risk".

ACT opposition leader Alistair Coe slammed Ms Palaszczuk's decision, saying he couldn't see how Canberrans could be considered a risk.

He said Mr Barr and Ms Palaszczuk - who are both Labor leaders - should be able to negotiate some solution, although he would not be drawn on whether that could include a "travel bubble" between the ACT and Queensland.

"I am very disappointed by the actions of the Queensland Labor Government," Mr Coe said.

"I think they have mischaracterised the ACT, they have lumped us in the same category as hotspots in Sydney or Melbourne - it shouldn't be that way."

Prime Minister Scott Morrison suggested Queensland had blindsided other states with its border closures.

"She'll make her decisions and I'll leave her to explain them and the medical advice upon which it's based," Mr Morrison told 2GB.

"These decisions should be driven by that advice and nothing else and there should be transparency around that.

"The arrangements between NSW and Victoria came as the result of a very open discussion between Gladys Berejiklian, Dan Andrews and myself and that then flowed onto how are we going to manage those things on the borders, which has actually been quite difficult in a lot of those border towns and not without some frustrations."

Mr Morrison also said,"borders are not a substitute for having a strong public health response".

"You can't just put the border up and think we'll be fine back here, we don't have to social distance, we don't have to be careful about how we engage in workplaces and we can all shake hands and hug up here. No you can't."

Deputy Chief Medical Officer Michael Kidd said it was up to the Queensland government to justify including the ACT in the border closure.

"The challenge, I imagine, is because of the open border between New South Wales and ACT," he said.

"There is nothing at the moment to stop people from moving between those two jurisdictions."

Queensland Deputy Police Commissioner Steve Gollschewski said a man allegedly drove from a Sydney hotspot to Canberra to catch a flight into Brisbane and onto Cairns.

"That person has expressed they were frustrated with the restrictions, didn't like them and wanted to go to work," he said.

Deputy Commissioner Gollschewski said it was a "selfish" act and the man would face court.

"While our system is working quite well we recognise we cannot keep this up with the types of numbers that are coming in," he said.

"Unless people have an exemption or a pass for freight, or are a cross border resident ... they will be 100 per cent stopped ... on both our road borders and our air borders."

Visitors will be denied entry except for "rare" exemptions.

Since last month, anyone from declared COVID-19 hotspots including Victoria and 34 NSW Local Government Areas, mostly around Sydney, was not allowed into Queensland.

NSW has been dealing with a resurgence of COVID-19 cases in recent weeks with new case numbers hitting double figures daily.

However, the ACT has no active cases of COVID-19 and a new infection has not been reported for three weeks.

Deputy Premier Steven Miles said everything changed for the state a week ago, after 63 days of no community transmission.

"A lot can change in a week, and we've seen in other states how it only take one case to see a widespread outbreak," he said.

In the past week Queensland reported nine new cases including two travellers from Victoria, three cases of local transmission and two Queenslanders returning from Sydney.

One new case was reported on Wednesday but the source is not known.

"Those cases have placed an enormous burden on our health system," Mr Miles said.

- with Dan Jervis-Bardy