The nation's chief medical officer warned the federal government stranded Australians could die if his recommendation of an Indian travel ban was accepted.
Paul Kelly also advised Health Minister Greg Hunt to use biosecurity laws, for the first time, with penalties of up to five years' jail and fines of $66,600.
While Professor Kelly said on Monday he gave the government no advice on fines or jail, his letter to Mr Hunt specifically notes the penalties.
He told the minister he was satisfied it was necessary to make it an offence for a person to enter Australia if they had been in India in the preceding 14 days to control the spread of coronavirus.
The chief medical officer said the biosecurity laws should only be used for as long as necessary in line with a pause on all flights until at least May 15.
"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," Professor Kelly wrote.
"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."
Mr Hunt said the advice was accepted because of the risk of deaths in Australia.
"Ultimately these decisions are taken to save lives and protect lives. This was a decision to potentially prevent a third wave in Australia," he said.
The advice - revealed at Senate estimates on Monday - contradicts the chief medical officer's claim he didn't recommend the threat of jail or fines.
The government has copped strident criticism from doctors, human rights groups and the Indian-Australian community over the punitive measures.
Prime Minister Scott Morrison defended claims of racism but agreed the measures would be reviewed this week amid a major backlash.
"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," Mr Morrison told 2GB radio on Monday.
"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."
There are about 9000 Australians in India who want to return home with 650 considered vulnerable.
Australian Medical Association WA president Andrew 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."
Labor frontbencher Bill Shorten said it was another sign "the government is definitely losing its soul".
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.
Australia will send an extra 1000 ventilators to India in a move Mr Hunt said recognised the human tragedy and agony of the situation.
Australian Associated Press