Gary Newman travelled to India to visit friends in March last year and has been unable to return.
The urgent application filed in federal court in Sydney will be held this afternoon.
Mr Newman is being represented by Michael Bradley and Chris Ward SC, who are working pro bono to overturn the travel suspension.
“The constitutionality of a proposed law criminalising return of Australian citizens from particular specified countries is deeply questionable,” Dr Ward tweeted earlier this week.
The lawyers will argue the emergency declaration is invalid because of an implied freedom to be able to return home.
Health Minister Greg Hunt declined to comment on the case when holding a press conference in Melbourne earlier this afternoon.
He said the “pause” in arrivals from India was working.
“More than one in eight passengers on the most recent flights were testing positive,” he said.
“That’s the level beyond anything that we had seen before.
“Our job is to protect Australia against a third wave, our job is to protect our health system.”