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The prime minister has shut down accusations the fine and jail time for returning Australians who have visited India in the past fortnight are racist.
The harsh rule was announced following Friday's National Cabinet meeting, which decided on a ban of indirect flights from India via Doha, Dubai, Kuala Lumpur and Singapore.
Prime Minister Scott Morrison has subsequently faced criticism from doctors, human rights groups and the Indian-Australian community over the strict measures.
Responding to some of his critics on Monday, he denied racist ideologies had anything to do with the decision.
"This is about health," Mr Morrison told 2GB radio on Monday.
"It's being put in place to ensure we do not get a third wave here in Australia and that our quarantine system can remain strong.
"I understand the measures have strong sanctions with them, but we've had the Biosecurity Act in place for over a year and no one's gone to jail."
The prime minister remained adamant the powers will not be used irresponsibly.
While Mr Morrison and senior ministers have pointed to health advice as the basis of the decision, Chief Medical Officer Paul Kelly said the powers already existed.
"There was no advice given in relation to the fines or jail terms, that's just how the Biosecurity Act works," he told ABC radio on Monday.
"Our advice was that we needed to do something about the number of positive cases coming into our hotel quarantine because of the risk of incursions."
Hundreds of vulnerable Australians trapped in India
There are about 9000 Australians in India who want to return home, including 650 considered vulnerable.
Australian Medical Association WA president Andrew Miller said similar measures were not in place for people in Europe or the UK during serious coronavirus outbreaks.
Dr Miller said it would be viewed as a dark period in the nation's history.
"It's not Australian to trap people overseas," he told the Nine Network.
"To suggest that a particular segment of the community should get fined for this is absolutely unacceptable and outrageous."
He apologised to Indian-Australians that he wasn't able to do more to stop the imprisonment and fine powers being used.
Call for government to prove move is not discriminatory
Mr Morrison said it was a temporary arrangement in place while quarantine and testing are strengthened.
"I want to get those repatriation flights running safely again. These are the things I have to do to ensure we can do that," he said.
Yadu Singh, a Sydney cardiologist and president of the Federation of Indian Associations of NSW, said the government had a moral obligation to help its citizens.
"There is a panic. There is a worry because coronavirus is a big, big problem in India and these people are stranded," he told ABC radio.
India is recording about 400,000 new coronavirus cases each day but the real number of people contracting it is believed to be higher.
The Australian Human Rights Commission wants the government to prove its decision to fine or jail Australians is not discriminatory.
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