Bangalore-based Gary Newman had claimed Health Minister Greg Hunt didn't have the power to interfere with a citizen's right to return home to Australia under the constitution.

But by agreement with the minister, he discontinued the Federal Court proceedings on Friday without progressing that argument to hearing, the law firm representing him confirmed.

Mr Hunt has said the ban, criminalising Australians' return to the country if they've been in the past 14 days, will not be renewed once it lapses at midnight on Saturday.

"Pursuing the litigation further at this time would not serve a useful public purpose," Marque Lawyers managing director Michael Bradley said in a statement.

The Federal Court on Monday rejected two other grounds of Mr Newman's challenge, which claimed Mr Hunt had failed to ensure the ban was no more restrictive or intrusive than required and that the Biosecurity Act wasn't clear enough to override Australians' common law right to enter the country.

Lawyers for Mr Newman has asked the court to determine those grounds before moving to the constitutional issues.

Those final two grounds claimed the minister did not have the power to interfere with a citizen's right to return home to Australia, either because of an implied constitutional freedom attaching to citizenship or because the constitution does not give the federal government legislative power to interfere with the fundamental right of return.

"The question is left hanging," Mr Bradley told AAP.

"If they do try it on again, we would be as concerned as we were this time."

Prime Minister Scott Morrison said the controversial 'pause' on India flights had worked, after active cases of COVID-19 in hotel quarantine dropped by nearly half over the past few weeks.

"The pause gave our quarantine system much-needed breathing space to minimise the risk of COVID-19 getting out of quarantine into the community and having a third wave here," Mr Morrison said.

"It's all about keeping Australians safe and ensuring we can keep living the way we are ... which is like few other countries in the world."

More than 70 Australians booked on the first repatriation flight out of India will miss out after they either tested positive or were deemed a close contact on Friday.

The plane, due to land in Darwin on Saturday morning, has a capacity of 150.

Labor senator Penny Wong said the situation was "beyond heartbreaking".

Australian Associated Press