An Australian man in India who tested positive to COVID-19 and will not be able to return on a repatriation flight tonight says he did "everything to protect himself" from the virus. 

About half of the 150 seats on a repatriation flight set to leave India will be left empty after more than 40 people tested positive to the virus, meaning they and their close contacts cannot fly.

The flight is due to leave New Delhi on Friday night local time, and arrive in Darwin on Saturday morning, and will be the first to leave India bound for Australia since the federal government imposed a ban last month.

Sunny Joura, who was booked on the flight but had tested positive, said he had not left his house in weeks.

He said he believed he contracted the virus either travelling to the hotel or during his time in the hotel.

"I have done everything to keep myself protected, double masking and everything," he said.

Mr Joura called on the Australian government to "get your act together" and create more quarantine facilities so that international passenger caps could be raised.

"I'm not saying that if I'm positive take me on the flight, but there were opportunities in the past, this is the third time my flight got cancelled," he said.

Australia's High Commissioner to India Barry O'Farrell said all passengers were made aware of the increased testing rules required to fly back to Australia.

"Obviously, I'm disappointed, as are those Australians who will not be on today's flight," he told the ABC.

"My team has worked hard across India to get them bookings on this flight because they are vulnerable.

Mr O'Farrell said anyone who had tested positive would still be considered vulnerable and be given priority on future flights.

"Regrettably those people will have to return home and deal with the COVID that they have, or continue to isolate to prove that they don't have COVID," he said.

Mr O'Farrell said people who had been signed on to the flight had all been put up in hotels, paid for by Qantas, so that they could do the first round of pre-flight testing, and that the results of the second round had not come back yet.

It may mean there are more people who are not allowed to fly.

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10,000 people seeking repatriation flight

There are about 10,000 Australians, permanent residents and their immediate family members seeking to return home from India.

Almost 1,000 of those are considered vulnerable. 

The federal government introduced the India travel ban a fortnight ago to help quarantine facilities, including Howard Springs in Darwin, deal with a high infection rate of returned Australians from India.

The passengers will fly back on a Qantas plane the federal government used to fly more than 1,000 ventilators and other essential medical supplies. 

That plane left Australia overnight.

It was the second planeload of equipment the federal government had sent to India to help some of the millions of people who have contracted COVID-19 there.