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Australia’s chief medical officer Paul Kelly says he did not provide specific advice to government around fines and jail time for people returning home from India, but provided health advice on “how to keep Australians safe”.

The Morrison government says its controversial decision to criminalise returns to Australia from India as the country battles a Covid-19 humanitarian disaster was “entirely founded in the advice of the chief medical officer”.

But Kelly drew a distinction on Monday morning, saying “our advice was the public health advice about the situation” and “I didn’t advise anything in relation to fines or any of those other matters”.

Under biosecurity regulations enacted to manage the pandemic, the health minister has sweeping powers, including scope to determine biosecurity emergencies.

These powers allow the minister to “determine any requirement that he or she is satisfied is necessary” to prevent entry or spread of disease. Offences of failing to comply are also punishable by five years in prison or a fine of more than $60,000.

Kelly said on Monday what health authorities were asked for on Friday “was public health advice, and once a decision is made by government as it was done on Friday night, there is another section of the [Biosecurity Act] which talks about what happens if you breach those things”.

“We weren’t asked about penalties – that’s [in] the law,” he said.

At a Senate estimates committee hearing on Monday morning, the secretary of the health department, Brendan Murphy, also confirmed the medical advice to the government on pausing travellers from India did not include specific recommendations on criminalising breaches.

But Murphy echoed Kelly’s point that the Biosecurity Act had existing legal sanctions “built into it”.

Murphy said Kelly had provided advice to the minister for health, Greg Hunt, on the need to temporarily pause people coming back from India including the use of a determination under the Biosecurity Act. While there was no specific recommendation around criminalisation, the Act had existing sanctions for breaches built into it.

“The advice as I said before was around the use of the Biosecurity Act to protect Australia from people coming back from a high-risk country. There was no specific advice on criminalisation.”

Members of the Senate committee asked Murphy to table the medical and legal advice that was provided to Hunt on Friday.

Murphy confirmed a legal brief prepared by the Department of Health accompanied the health advice informing the decision, but he did not table the material. He took the request on notice. He said the government would consider whether the legal advice may have legal privilege attached to it.

The government’s decision, which became known early last Friday evening, and was then announced formally by Australia’s health minister at midnight, has generated a public furore.

The extraordinary and unprecedented move appears to have been triggered by the return of two Australian cricketers from India after a ban on direct flights took effect. The cricketers came home by transiting through Qatar.

Australia’s national vaccination is running behind schedule, and there has been a debate for months about whether hotel quarantine remains the best method for infection control during the pandemic, or whether it would be better to house returning travellers in purpose-built quarantine facilities.

The Australia Human Rights Commission issued a statement on Saturday saying the decision to use the Biosecurity Act to impose a temporary ban on citizens returning home “raises serious human rights concerns”.

“The need for such restrictions must be publicly justified,” the commission said. “The government must show that these measures are not discriminatory and the only suitable way of dealing with the threat to public health”.

Law professor Kim Rubenstein from the University of Canberra said people directly affected by the measure would have scope to challenge the regulations in the federal court.

Rubenstein noted the powers in the biosecurity regulations were subject to safeguards. Theses included that the requirements imposed by the health minister must be “likely to be effective”, be “appropriate and adapted” to its purpose and be “no more restrictive or intrusive than is required in the circumstances”.

Criminalising returns to Australia from India comes despite the country reporting fewer coronavirus cases per capita than either the US or the UK during their respective Covid peaks.

Over the weekend, the foreign affairs minister, Marise Payne, said the move was “not in any way” motivated by racism.

Payne said on Sunday the decision had been made “under the Biosecurity Act on the basis of advice from the chief medical officer” and was a “temporary pause on returns”.

She said the decision was “entirely founded in the advice of the chief medical officer”.

On Monday, the prime minister Scott Morrison said imposing the restrictions had been a “difficult decision”, and he thanked Australians of Indian descent for their “patience and understanding”.

“Yes, I understand the measures have strong sanctions with them but we’ve had the Biosecurity Act in place now for over a year, and no one’s gone to jail,” Morrison told 2GB.

“There hasn’t been any irresponsible use of those powers that are used very, very carefully, and I can assure people that they will be used appropriately and responsibly.”

Morrison said the pause in flights from India was temporary and the decision would be reviewed this week and next week. “This only needs to be there in place for as long as it needs to be there to keep Australians safe,” he said.

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