The federal government has been heavily criticised for .
The Australian Human Rights Commission has called on the government to prove its decision to fine or jail Australians is "not discriminatory".
It says it holds deep concerns about the "extraordinary" new restrictions.
Human Rights Watch, meanwhile, has described the move as "outrageous".
Travellers from India have been blocked from entering Australia until at least 15 May, when the decision will be re-assessed.
Indirect routes via Doha, Dubai, Kuala Lumpur and Singapore have also been closed off, as .
Health Minister Greg Hunt says anyone attempting to defy the rules will be hit with fines of up to $66,600, five years in prison, or both.
More than 9,000 Australians in India are registered as wanting to return, including 650 considered vulnerable.
"The need for such restrictions must be publicly justified," the Human Rights Commission said on Saturday.
"The government must show that these measures are not discriminatory and the only suitable way of dealing with the threat to public health."
Human Rights Watch's Australia director Elaine Pearson says Australians "have a right of return to their own country".
Kylie Moore-Gilbert, an Australian academic recently freed from two years in detention in Iran, called the move "immoral, unjustifiable and completely un-Australian".
"I know what it means to do time for absolutely no reason whatsoever," she wrote on Twitter. "I also know what it means to be rescued from a COVID-riddled overseas hellhole and be brought back to Australia [into quarantine]."
Former race discrimination commissioner Tim Soutphommasane said there appeared to be “different standards” for arrivals into Australia depending on where they had come from.
“Last year when Covid raged it was fine to accept those coming from the US, but those from China were sent to Christmas Island,” he tweeted. “Now, it looks like those seeking to return from India aren’t only prevented from that, but subject to criminal penalties. So why the different standards?”
Labor MP Jason Clare has backed the flight ban as the "right call" but questioned the decision to criminalise citizens for trying to return home.
The government's decision was based on the number of positive cases from India detected in the country's quarantine facilities, Mr Hunt said. More than 150 overseas-acquired infections have been reported Australia-wide in the past week, many from India.
"The government does not make these decisions lightly," he said in a statement on Saturday.
Treasurer Josh Frydenberg on Saturday defended the move, conceding it was “drastic” but would ultimately “keep Australians safe”.
Foreign Minister Marise Payne is also standing by the announcement, which she said was “entirely founded” on health advice.
"We absolutely recognised the very, very difficult circumstances occurring in India right now … for so many families, and indeed here in Australia, for Indian Australians, who are so worried about their families overseas,” Senator Payne told reporters in Canberra on Sunday.
More than 200,000 people have died and India has been setting records each day with the tally of new cases.
The Department of Foreign Affairs and Trade said on Saturday it was supporting 372 consular clients in India, three of which are COVID-19 related. SBS News has sought further information.
Around 20,000 Australians registered with DFAT have returned from India since March last year.
The government is sending oxygen supplies, ventilators and personal protective equipment to India through DFAT.
Additional reporting by AAP.
