Neela Janakiramanan, an Australian surgeon with family in India said the decision to "criminalise" Australians returning from India was disproportionate and overly punitive.
India set another world record on Thursday with more than 379,000 new cases and 3645 deaths.
From Monday, anyone who has been in India within 14 days of their intended arrival date in Australia will be banned from entering the country.
Meanwhile, on Friday, Australia extended the ambit of flight ban from India by shutting transit routes through Doha, Singapore and Kuala Lumpur, ABC News reported.
"India, there needs to be a suspension", Premier Mark McGowan told reporters in Perth, ahead of the federal government's decision. The law allows the government to take any necessary measures to prevent and control Covid-19, to protect the health of all Australians. British and Irish nationals arriving in England from India must quarantine in a hotel.
It's intensified calls for more to be done to get Australians home, reports the BBC's Frances Mao from Sydney.
Some Australians, including cricketers Adam Zampa and Kane Richardson, reportedly took advantage of a loophole to return from India via Doha.
More than 9000 Australians in India are registered as wanting to return, including 650 people registered as vulnerable.
Hospitals are running low amid surging cases of Covid-19.
The worsening Covid-19 crisis in India has spiralled in recent weeks.
India has seen cases soar to 19 million and deaths total 200,000.
"The risk assessment that informed the decision was based on the proportion of overseas travellers in quarantine in Australia who have acquired a COVID-19 infection in India", Mr Hunt said in a statement.
India registered 386,452 new coronavirus cases on Friday, yet another global record high for infections in a single day. "However, it is critical the integrity of the Australian public health and quarantine systems is protected and the number of COVID-19 cases in quarantine facilities is reduced to a manageable level", Mr Hunt said.
The country reported zero new cases of community transmission on Tuesday.
"National cabinet expressed solidarity with the Indian community both within Australia and overseas", Australian Prime Minister Scott Morrison said in a statement yesterday, not fronting the media after the meeting. India has the world's fastest-growing caseload.
The government is sending oxygen supplies, ventilators and personal protective equipment to India through the Department of Foreign Affairs.