Victorian MPs and senators could be forced to isolate in Canberra for two weeks before federal parliament returns on August 24.
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However, Labor has proposed an alternative model involving some members being allowed to video-call into parliament.
Acting Chief Medical Officer Paul Kelly, who proposed the isolation model, said travelling Victorian politicians posed a significant risk to the local community.
"It also presents a significant risk for members and senators and their staff from other jurisdictions, with the possibility of seeding into other jurisdictions," he wrote to the prime minister on Thursday.
"It also presents a risk to those who are themselves vulnerable, those at increased risk if infected with COVID-19."
To reduce this risk, Professor Kelly says Victorians should apply for an exemption to travel to the ACT, and then follow a strict 14-day period of quarantine.
He says the quarantine period could also occur in Victoria as long as strict conditions were adhered to, including having a coronavirus test on day 12 and awaiting the result before ending isolation.
Prof Kelly said MPs and senators must be informed by this Saturday, so they have enough time to quarantine.
He's also concerned about community transmission in other parts of the country, mainly Sydney, noting Canberra has no known community transmission.
The advice is being considered by a group tasked with setting safety standards for parliamentary sittings.
Speaker Tony Smith, a Victorian himself, has advised politicians to seek extra advice on attending parliament from party whips, the Independent Parliamentary Expenses Authority and the Department of Finance.
Other Victorian-based federal MPs include Treasurer Josh Frydenberg, Health Minister Greg Hunt, Senate President Scott Ryan, Education Minister Dan Tehan and deputy Labor leader Richard Marles.
Labor leader Anthony Albanese has put forward the idea of a "hybrid system", whereby members could participate by video link if they wanted to speak on legislation, ask questions or answer questions.
A quorum would still be needed on the floor of the parliament, and voting would still require physical presence.
The measure would last only as long as pandemic restrictions were in place.
"We believe this is a practical solution to the emergency circumstances," Mr Albanese said.
Australian Associated Press