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Photograph: Steven Hoare/Getty Images

The Australian government needs to do more to avoid a repeat of the scores of seats left empty on the first post-ban repatriation flight from virus-ravaged India, one community leader has said.

Eighty Australians touched down in Darwin on Saturday morning and were moved to the Howard Springs quarantine facility on the city’s outskirts.

But about 70 seats reserved for returning Australians were empty after 40 people tested positive before the flight from Delhi, with another 30 identified as close contacts.

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Dr Yadu Singh, the president of the Federation of Indian Associations of New South Wales and the head of the Council of Indian Federations of Australia, said: “They need to think about a different mechanism so as not to waste those seats.”

Total cases of Covid-19 have topped 24 million in India, with the country’s prime minister, Narendra Modi, saying the country was “on a war footing” as more than 4,000 people died from the virus for a third straight day.

India is experiencing a spread of cases associated with the B.1.617 variant, which some experts say could be more transmissible than other variants. The World Health Organization this week declared it a “variant of concern”.

Indian community leaders in Australia said statewide lockdowns in the subcontinent and higher case numbers in cities was making the job of repatriating Australians harder.

Some 10,000 Australian citizens and permanent residents have told the government they want to return from India. First in line for repatriation flights are about 1,000 people the government has deemed vulnerable.

Singh said he sympathised with the people who were blocked from travelling, but it was the right decision to protect other people.

He said: “I’m very pleased the flight has arrived. But what they could do differently is have a mechanism to bring people to the city where the plane is leaving and have them in quarantine and test them several times.

“I hope they will learn from what has happened and have a better testing system to bring as many as possible home. They are Australian citizens and there are moral obligations to look after them.”

The Department of Foreign Affairs and Trade declined to answer Guardian Australia’s questions about whether efforts had been made to fill seats that became available on the repatriation flight and if a standby system would be in place for future flights.

The department also did not say if the government had plans to set up quarantine for Australians stuck in India to isolate before the flight.

“Dfat’s highest priority at this time is helping vulnerable Australians overseas,” a spokesperson said in their response.

Related: Half-empty India repatriation flight lands in Darwin after travel ban lifts

Saturday’s flight into Darwin was the 39th government-facilitated flight from India, but the first since the Morrison government imposed a ban after cases surged in India. The ban came with a threat of jail under the Biosecurity Act for any Australians trying to return home from the country.

The next repatriation flight is due to arrive on 23 May and Dfat has said arrangements for further flights are under way.

Singh, a cardiologist, has about 70 relatives – including brothers, uncles, aunts and cousins – living in India. He has lost family members to the virus.

“Each time I get a call from India I worry. It is very hard,” he said.

There are almost half a million Indian-born people living in Australia and about half are Australian citizens.

Singh said his own anxiety about his family’s safety was repeated among people with Indian heritage all across Australia.

He said: “I’ve been to Hindu and Sikh ceremonies worshipping dead relatives. I sit there and pray along with them.

“Everyone has a family member going through a difficult time, but they can’t do much because they’re 10,000km away.”

Sury Soni, the president of the Federation of Indian Associations of Victoria, said he had been told by Australia’s high commission in India that they were working to put vulnerable people on standby for flights.

He said state lockdowns across the country imposed a week ago were making it harder for people to travel, and many were worried travelling for flights would mean they had to enter quarantine in metropolitan areas where cases were higher.

“Even a facility in New Delhi couldn’t keep people waiting there for months,” he said.

He understood there were up to 900 Australians identified as vulnerable in India. These people were either elderly, had existing medical conditions that put them at higher risk, or who needed to be in Australia to care for family members.

Related: Indian Covid variant: which countries have highest infection rates?

The federal opposition leader, Anthony Albanese, said on Saturday there were still 30,000 Australians stranded overseas.

“It’s extremely distressing for those Australians with loved ones trapped overseas for more than a year. Scott Morrison promised to bring them home and he hasn’t.”

The treasurer, John Frydenberg, said the high commission was working with Australians in India. “We are dealing with a situation where we are seeing more than 800,000 new Covid cases [globally] a day with new variants of the virus.

“We did see a spike in the number of cases when people from India were coming. We invoked the biosecurity act and we then reassessed it after a couple of weeks, and the flights have now started and that’s a positive development.

“But again we have to maintain our health settings because we know how damaging both to the lives and livelihoods of Australians an outbreak here would be.”

In a statement released before Saturday’s flight arrived, the government said the flight was part of a $37.1m support package for India.

More than 15 tonnes of medical supplies had been sent to India, including more than 2,000 ventilators and 100 oxygen concentrators.