The government said 80 people arrived in Darwin on Saturday, and would be quarantined for a fortnight.
Their Qantas flight was originally scheduled to carry 150 people onboard.
But 70 passengers were later barred from travel after testing positive for coronavirus or coming into close contact with others who were.
Australia's strict rules on pre-flight testing meant there was not enough time for the seats to be given to others waiting to return.
Treasurer Josh Frydenberg said there would be more capacity for people to return to Australia on other flights scheduled in May.
"We're following the medical advice and ensuring that we protect Australians here," Mr Frydenberg told reporters. "We've got to maintain our health settings because we know how damaging to the lives and livelihoods of Australians an outbreak here [can be]."
He added that Australia's High Commission was working to help other Australians stranded in India, and at least 9,500 had registered as wanting to return.
The Australian government announced the flights following an outcry over a three-week ban on all arrivals from India - a country dealing with one of the world's largest outbreaks of coronavirus.
But critics have said the proposed rescue effort is too small and excludes most Australians stuck in India. They've called on the government to allow more commercial airlines to fly from India to Australia.