Former Australian Guantanamo Bay detainee Mamdouh Habib could have been abused while in custody in Egypt, said Foreign Minister Alexander Downer.
Mr Habib spent nearly three years at Guantanamo Bay
He added that although there was no evidence he was also tortured by US authorities, he could not rule it out.
Mr Downer's comments were in response to Mr Habib's first television interview since his release in January.
In a programme broadcast on Sunday, Mr Habib said he had been beaten and sexually assaulted while in custody.
The former taxi driver spent more than three years behind bars after being arrested in Pakistan in the wake of the 11 September 2001 attacks.
Mr Habib was detained in Egypt and Pakistan before being sent to Guantanamo Bay. He was released without charge in January 2005, when US officials said they did not have enough evidence against him.
"For all I know, he may have been badly treated in Egypt, but we don't know because the Egyptians have still not conceded to us that they held him," Mr Downer told Australian radio on Monday.
He also said that while there was no proof Mr Habib was tortured by US authorities, a new investigation might yet find evidence of maltreatment at Guantanamo Bay.
In his first interview since returning home in January, Mamdouh Habib strongly denied any links to terrorism.
Born in Egypt, but has lived in Australia since 1980
Arrested in Pakistan after 11 September attacks
Flown to Egypt, where his lawyer says he was tortured
Transferred to Guantanamo Bay in May 2002
Released January 2005
"I've been through a lot. I've been harmed, for no reason. I'm innocent," he told Nine Network in a special Sunday evening programme.
He also said he suffered constant abuse both before and after his transfer to Guantanamo Bay.
He said the torture began almost immediately after his capture in Pakistan, in October 2001.
He said that on one occasion, an Australian government official watched him being beaten and did nothing to stop the abuse.
After three weeks in Pakistan, Mr Habib was sent to Egypt, where he said the abuse continued.
He said he was beaten, subjected to electric shock treatment and given drugs.
On his arrival at Guantanamo Bay in May 2002, Mr Habib said: "They put me in isolation all the time. I never saw the sun, I never had a shower like a human being. I never had soap. I never had a cup to drink. I was never treated like a human being," he said.
He also alleged he was once smeared with the menstrual blood of a prostitute.
"She threw it in my face," he told Nine Network.
Mr Habib was originally detained after US officials alleged he trained with al-Qaeda and had prior knowledge of the attacks in New York and Washington.
At some stage during his capture - the exact location is unknown - Mr Habib confessed to training the 11 September hijackers, a confession he now says is false and was made purely "to save myself" from further abuse.
Mr Habib said that, at the time of his arrest, he was in Pakistan looking for schools, as his family was considering moving there.
But during Sunday's interview he refused to answer questions about whether he had been to Afghanistan, and if so, who had funded any trips.
He said he would only answer questions on this issue before a judge.
Mr Habib is planning to go to court to clear his name and persuade the Australian authorities to give him his passport back.
On his return to Sydney in January, the authorities said Mr Habib remained under suspicion, and warned his activities would be constantly monitored to ensure he did not become a security threat.