The Chief Medical Officer says Scott Morrison's staff is responsible for ensuring he adheres to quarantine advice in Canberra.
Paul Kelly made the revelation despite earlier warning an influx of Sydney-based politicians posed a "significant risk" to ACT residents.
The Prime Minister is currently in 14-day quarantine at The Lodge, but has been granted exemptions to travel between the residence and Parliament House.
In a letter to Mr Morrison on July 16, Professor Kelly warned the outbreak in Sydney was "not improving" and had the potential to seed in the ACT.
He advised anyone travelling to and from The Lodge to undergo daily saliva testing, wear masks, and minimise contact with APH staff.
ACT Chief Health Officer Kerryn Coleman was not provided a copy of the letter, and had not signed off on it.
"The travel of members and senators who reside in Sydney to the ACT presents a significant risk to ACT residents, particularly those who work in the Australian Parliament House," Professor Kelly wrote.
But appearing before a Senate committee on COVID-19 on Friday, he conceded it was up to Mr Morrison's staff and department to ensure he complied with the advice.
"I have no statutory responsibility, but from time to time I'm asked for advice by the Prime Minister in relation to these matters," he said.
"How it's being actually operationalised and implemented is not my responsibility ... Advice is taken, and then how that is used is up to the individual."
Professor Kelly agreed with Labor senator Katy Gallagher's suggestion the arrangement operated on "some goodwill and through negotiations".
He insisted the Commonwealth was working "in collaboration with ACT Health", with regulations on the Parliamentary Triangle complicating enforcement.
Parliament is due to sit on August 3 for two weeks, though NSW's COVID-19 crisis prompted fears the virus could travel to the capital before spreading across the country.
Professor Kelly's letter suggested "significant additional mitigations" were needed to counter the threat of an outbreak in Parliament, which was operating at "near normal function and capacity".
"A transmission event within APH also has the potential to impact the function of government due to quarantine and isolation requirements, as well as the broader public health restrictions required by ACT Health," he said.
Preventing the public visiting Parliament, a review of density requirements within the building, and APH staff working from home would all be need to be implemented, he said.
"With these extra precautions, a very small, but not zero risk would remain that COVID-19 could be seeded into the ACT community," he wrote.
Senator Gallagher wrote to Professor Kelly to clarify Mr Morrison's arrangements on Wednesday, the same day he held a press conference at The Lodge.
"I was concerned to see the face-to-face press conference conducted today at The Lodge with several individuals entering an apparent quarantine zone," she said.
"Canberrans, like all Australians, have sacrificed a lot over the past 18 months throughout the pandemic. I am very concerned that risks presented by those who are arriving in the ACT from Covid-affected areas, such as greater Sydney, are managed appropriately and without favour."
Professor Kelly outlined advice for press conferences to be held outdoors, with strict mask use, and preferably attended by fully vaccinated people.
A number of journalists who attended Wednesday's press conference were not fully vaccinated.
Sydney-based MPs wanting to attend in person were already in 14 days' quarantine, though many will attend remotely after failing to cross the border before the July 19 deadline.
