Former Guantanamo Bay detainee Mamdouh Habib and his wife have had their passports confiscated and been interrogated about "security issues" over several hours at Istanbul's international airport.

Mamdouh and Maha Habib flew to Turkey from Beirut, and were stopped at Customs on arrival.

Their passports were taken away and they were taken to a holding room within Istanbul airport.

They were interviewed over 12 hours and then put on a flight to Beirut without their passports.

Mr Habib's lawyer Stephen Hopper said the couple were asked a series of questions about suspected jihadists Mathew Stewart and and Jamal al-Harith.

"We have been given no water, no toilet, Mamdouh is sick ... we are stuck here," Maha Habib said.

Mr Habib told the ABC that a Lebanese man who described himself as an employee of ASIO questioned him.

He said Turkish officials took away his phone, US$9,000 in cash, pushed and threatened him.

"They wanted to talk about Mathew Stewart," Mr Habib said.

Mathew Stewart was an Australian soldier who joined Islamic militants in Afghanistan 15 years ago.

It had been reported that Stewart was killed in a US air strike over a decade ago.

But earlier this week an Al Qaeda affiliated magazine, al-Risalah, published an interview with a man calling himself Hamza Australi, who it said was fighting with militants in Syria.

Senior members of Australia's counter-terrorism community believe Hamza Australi may be Stewart.

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Mr Habib wrote about meeting Stewart in a book he wrote following his incarceration in Guantanamo Bay on terror charges, which were dropped.

"ASIO wanted to talk about Mathew. But I don't want to talk to ASIO, why should I? I am a free man," Mr Habib said.

Lawyer Mr Hopper has been in phone contact with the pair.

"They were taken away and interrogated by people wearing suits," he said.

"We assume that it's Turkish security. They weren't wearing military uniforms or police uniforms.

"They were asked a number of questions pertaining to security issues."

Mr Habib said he had contacted the Australian ambassador in Turkey and his lawyer had contacted the Department of Foreign Affairs and Trade.

The Habibs have since landed back in Beirut.

Maha Habib said they were told that they could collect their belongings and passports from immigration staff when they arrived back in Lebanon.

"Mamdouh needs medical attention," she said.

After the Habibs returned to Beirut DFAT issued a statement saying they had both been offered consular assistance.

"Embassy officials in Beirut will continue to provide appropriate consular assistance in line with the Consular Services Charter," the statement read.

"Out of respect for their privacy, we will not provide further details."