Chief Medical Officer Paul Kelly says there is a "very small, but not zero risk" the return of parliament could seed COVID-19 into the ACT.
MPs and senators are due to return to Canberra on August 3 for parliamentary sittings, which run for most of the month.
Professor Kelly has provided written advice to the prime minister on how parliament could be resumed safely.
In the advice, tabled at a committee hearing on Friday, he said the travel of Sydney-based members and senators to Canberra presented a "significant risk to ACT residents".
He also noted a transmission event in Parliament House had the potential to "impact the function of government due to quarantine and isolation requirements".
But Professor Kelly said he and ACT Chief Health Officer Dr Kerryn Coleman had reached an understanding on guidelines to minimise the risk of coronavirus transmission from MPs and staffers entering the ACT.
They include pre-parliament quarantining of MPs, daily saliva tests, mask wearing and social distancing.
Scott Morrison has been living in The Lodge under tight restrictions including daily testing, but has been able to drive to his office in Parliament House.
Asked how he was monitoring Mr Morrison's compliance with the advice, Professor Kelly told the committee: "I am not monitoring it."
He said restricting the business of MPs could be in breach of the constitution.
"There are parts of the constitution which actually say that no one has the power to stop MPs doing what they need to do to."
He said the prime minister's office and department would be responsible for implementing the conditions.
Australian Associated Press