Australia will lift a ban on its citizens returning from COVID-hit India from next Saturday and the first repatriation flight will land in the city of Darwin the same day, Prime Minister Scott Morrison said on Friday.

The Australian government, for the first time in history, recently imposed a temporary ban on its citizens from returning home, if they have spent time in India up to 14 days before flying back.

The government threatened to prosecute them with a possibility of five years of jail term or a penalty of 66,000 Australian dollars (USD 50,899).

The move triggered a backlash with several lawmakers, doctors, civil societies and businessmen criticising the government for "abandoning" Australians in India and threatening the travellers with a hefty penalty and a jail term.

The government's order on the matter is set to expire on May 15.

Following the National Security Committee on Friday, Morrison agreed it saw "no need to extend it beyond that date".

Australia will charter three repatriation flights between May 15 and May 31. The first flight into Darwin will touch down on May 15. Direct commercial flights from India are still banned.

Morrison said flights being organised to repatriate stranded Australians will be "focused on bringing those Australian citizens, residents and families who have been registered with our high commission and consular offices within India."

"It will also be targeted (at) those 900 most vulnerable of the group," he said after the latest national Cabinet meeting.

"I have asked the Department of Foreign Affairs and Trade (DFAT) to do a review of those registrations those who been registered in India to ensure they are current. And that will assist a proper prioritisation of placing people on those flights," Morrison said.

''The charters will be undertaken by the Australian crews, and they will require rapid antigen testing prior to departure," he said.

He said that three flights will land in Darwin by the end of this month while Queensland, New South Wales and Victoria were also open to taking in more flights from India which means there could be six flights potentially.

Morrison, while addressing a media conference, said a three-week pause on flights from India has slowed the rate of COVID-19 infections in quarantine facilities.

''We have already facilitated the return of around 20,000 Australians from India, and this has been a big task. And that task will commence again on May 15, he said.

''All of this is about sensibly preventing a third wave of COVID-19 here in Australia, and doing that responsibly, while at the same time doing everything we can to sustainably bring Australians home from what is currently the most significant hot spot for those travelling into Australia of anywhere in the world right now," Morrison said.

"The biosecurity order is doing its job. It is doing what we intended it to do. It will run for the term we intended for it to run, and then that will be replaced by arrangements made beyond that point to ensure we can prevent the third wave,'' he said.

Media reports said that Morrison was due to speak to Prime Minister Narendra Modi later on Friday to see what further assistance Australia can give.

"I want to thank in particular, in Australia, our Australian community of people who are of Indian descent. The Indian community here in Australia. I thank them for their patience. I thank them for their understanding," Morrison said.

"...I know they will be welcoming the fact these repatriation flights will be returning once again but also believe we will be able to do that because of the actions we have taken on a sustainable basis," he added.

Official figures say there are currently 9,000 Australians in India who want to return home.

With a record 4,14,188 new coronavirus infections being reported in a day, India's total tally of COVID-19 cases climbed to 2,14,91,598, while the active cases crossed the 36-lakh mark, according to the Union Health Ministry data updated on Friday.

Meanwhile, Australia's chief medical officer Paul Kelly stood firm on advice on India travel suspension.

"With the data, we had in terms of the increasing cases coming from India, where they have had over 2 million cases in the past week, with thousands of deaths, the contrast between their expense and our experience, and I joined the prime minister in my heart going out to people in India and those with loved ones in India," Kelly said.

"We had to take that into account to protect Australia using the data we had last week. And it's working." Kelly said.

According to ABC news, many Australians have fled to Sri Lanka from India. The federal government is now working with Sri Lanka towards ensuring people who board flights to Australia have received a negative test.