The official medical advice to the Morrison government recommending “pausing” Australian arrivals from India also contained a blunt warning that those stranded risk serious illness and even death.

Chief Medical Officer Paul Kelly’s advice said: “It is important in any measures we implement that we balance the burden on our quarantine and health systems and the protection of our community with the need to help Australians to get home, including those currently residing in high risk countries”.

Kelly said COVID-19 continued to be “a severe and immediate threat” to health in Australia and India was a high risk country, with a sharp increase recently in the number and proportion of overseas-acquired cases coming from there.

“Each new case identified in quarantine increases the risk of leakage into the Australian community through transmission to quarantine workers or other quarantined returnees and subsequently into the Australian community more broadly,” Kelly wrote in his Friday advice to Health Minister Greg Hunt.

“This quarantine ‘leakage’ presents a significant risk to the Australian community.”

The advice was in relation to the government’s determination under the Biosecurity Act – announced in the early hours of Saturday – which makes it an offence for anyone to enter Australia if they have been in India in the preceding two weeks.

This was to close any loopholes enabling people to arrive via third countries after the government suspended flights from India until at least May 15.

Kelly said in his advice, running to more than three pages, that Australia’s quarantine and health resources to prevent and control COVID from international arrivals were limited.

“Due to the high proportion of positive cases arising from arrivals from India, I consider a pause until 15 May 2021 on arrivals from India to be an effective and proportionate measure to maintain the integrity of Australia’s quarantine system,” he said.

But Kelly was careful to put on record a clear warning about the dangers faced by Australians who could not get home.

“I wish to note the potential consequences for Australian citizens and permanent residents as a result of this pause on flights and entry into Australia.

"These include the risk of serious illness without access to health care, the potential for Australians to be stranded in a transit country, and in a worst-case scenario, deaths.”

However he said “these serious implications can be mitigated through having the restriction only temporarily in place, i.e a pause, and by ensuring there are categories of exemptions.”

Under the law, action taken must be no more restrictive or intrusive than necessary and in place only so long as needed.

The determination will expire on May 15 unless extended.

The exemptions include crews of aircraft and vessels and associated workers, Australian officials, defence personnel and diplomats and family members, foreign diplomats accredited to Australia and family members, and members of an Australian Medical Assistance Team (AUSMAT).

There are more than 9,000 Australian citizens and residents registered in India of whom 650 are considered vulnerable.

The advice pointed out this would be “the first time that such a determination has been used to prevent Australian citizens and permanent residents entering Australia”.

On Monday Kelly was anxious to say he had nothing to do with the penalties that exist for breaching the determination, which include large fines and up to five years prison and have received much negative publicity. His letter did note the penalties the act carries.

Scott Morrison told 2GB the arrangement was aimed at ensuring Australia did not get a third wave of COVID and its quarantine system could remain strong.

He downplayed the sanctions, saying they would be used appropriately and responsibly.

Morrison said people who had been in third countries for 14 days could return home to Australia. “But if they haven’t, then they have to wait those 14 days.”

Asked on the ABC whether the government should vaccinate Australians stranded in India, Kelly said: “It’s certainly worth looking at. I would say, though, that we know that many of the Australians that are in India at the moment, they’re very scattered. So it’s a huge country; being able to get to them would be a challenge”.

Queensland Nationals senator Matt Canavan has condemned the government’s stand, tweeting: