Prime Minister Scott Morrison on Friday said the travel ban on Australians returning home from coronavirus-hit India will not be extended beyond May 15, and repatriation flights will commence soon.

For the first time in history, the Australian government 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 government's order on the matter is set to expire on May 15.

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

"The original decision to put in place that biosecurity order until May 15 has proved very effective and it will run its full course until that time without any change," he said.

Morrison's remarks came a day after the ban was challenged in the federal court in Sydney by a 73-year-old Australian who has been stranded in Bengaluru since March last year.

"What we will be doing is receiving our first repatriation flight into the Northern Territory as part of the charter arrangements we have … to bring back those first people from India at that time," Morrison said.

Morrison said he anticipated three repatriation flights before the end of the month, with a focus on bringing back vulnerable Australians.

"In addition, there will be rapid antigen testing put in place for everyone getting on the flights," he said.

"The challenge we have had with arrivals from India is the higher incidence of infections and the stress that they were placing on the quarantine system." He said it was the smart, sensible, wise and compassionate thing to put the pause in place.

Morrison said it was unclear how many of the 9,000 Australians stranded in India had contracted the virus but said anyone boarding a repatriation flight would be required to test negative.

“We have rapid antigen testing in place to give ourselves a greater sense of surety that if we are bringing people back to Australia we are minimising the risk of Covid cases of being brought into the country,” he said.

New coronavirus cases and deaths in India hit a record daily high on Thursday after 4,12,262 new infections and 3,980 fatalities were reported, taking the total tally of Covid-19 cases to 2,10,77,410 and the death toll to 2,30,168.

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