The Federal Court has thrown out part of a challenge to a temporary ban on passengers travelling from India, where COVID-19 infections rates have been soaring.

Lawyers for Melbourne man Gary Newman, 73, who is stuck in India, told the court his common law right to return home had been contravened by the biosecurity order preventing people from returning to Australia if they have been in India for the past 14 days.

But government lawyers told the court the act prevailed over such rights if it was needed to protect the national interest. 

The case may not be over yet, with lawyers considering whether to pursue two other constitutional issues.

The government's controversial ban, which began on May 3 is due to finish on Saturday.

A question of rights

The ban carries the threat of criminal sanctions, including five years in jail and fines of up to $66,000 for people who try to return.

Mr Newman's lawyer, Chris Ward, told the court that refusing to let Australian citizens return was at odds with a well-established right.

He said the ban had a chilling effect by criminalising that right.

"Difficult decisions and difficult choices in times of crisis must still be governed by the rule of law," Mr Ward told the court.

But Craig Lenehan, who represented the Commonwealth, described the biosecurity act as a "legislative bulldozer".

"There's nothing in the statute to suggest that precise matters identified by my opponents needed to be taken into account for an emergency power directed to the national interest," Mr Lenehan told the court.

"The rights that are raised were intended to be impinged upon by the Parliament."

Justice Thomas Thawley agreed.

"It's hardly surprising the Parliament would provide a broad power to meet such threats," Mr Thawley told the court.

"Even at the cost of some rights."

He dismissed the issues raised in the case on Monday about the legality of the temporary ban.

The court agreed to hear the first half of the case as a matter of urgency ahead of the flights resuming on Saturday.

Mr Ward told the court he was concerned the matter would soon become a moot point, but that it was important to test the law ahead of any further developments.

Mr Newman's lawyers are still considering whether to raise constitutional issues about whether the Parliament had the power to create the biosecurity act.

Ban criticised as 'immoral and un-Australian'

The ban has been widely criticised since it was introduced, with some describing it as "immoral and un-Australian" and others questioning the legality of banning citizens from coming home.

Over the weekend the ban again came under scrutiny when an Australian permanent resident died after contracting COVID-19 in India.

The 59-year-old man died within days of the federal government banning Australian citizens and permanent residents from returning home.

But senior government ministers defended the ban, saying at the time it was based on expert medical advice and had been brought in to protect Australians.

Foreign Minister Marise Payne said more than half of Australia's hotel quarantine cases were arrivals from India, which put a burden on health services.

Prime Minister Scott Morrison also told Nine Radio at the time that the criticisms were similar to when the government decided to close the border to China early in 2020.