Members within former prime minister John Howard's own department are being investigated over their involvement in the overseas kidnapping, rendition and alleged torture of cleared terror suspect Mamdouh Habib.
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The Egyptian-born Australian was arrested in Pakistan in 2001, during the aftermath of that year's September 11 US attacks, and flown to his birth-country by the CIA.
He was detained there for six months, where he claims he was tortured horrifically by members of the now-deposed Mubarak regime.
Mr Habib was then transferred to Guantanamo Bay, held for three years, before being released in January 2005 and cleared of all charges.
After being freed, Mr Habib returned to Australia and sued the Federal Government, accusing it of direct involvement in his capture and being complicit in his torture.
The Federal Government paid Mr Habib an undisclosed sum of cash to drop the case, after damning evidence from an Egyptian prison guard claimed that an Australian official named ''George'' was present during the torture.
Late last year, the Inspector-General of Intelligence and Security was ordered to find out what Australian intelligence agencies, the Australian Federal Police and the Department of Foreign Affairs and Trade knew about Mr Habib's torture.
The intelligence watchdog's annual report, tabled in Parliament yesterday, reveals that Inspector-General Vivienne Thom wrote to Prime Minister Julia Gillard mid-way through the investigation, claiming to have evidence that the Attorney-General's Department and the Department of Prime Minister and Cabinet had been directly involved in the case. Dr Thom claimed that officers from both departments were ''directly involved in decision making at the time'' of Mr Habib's detention and torture.
She requested that Ms Gillard give her permission to pursue investigations against those departments, a request that was granted on February 26.
''The work of the inquiry has been substantial,'' Dr Thom said in the report.
''By the end of the reporting period, a small team of four had examined many thousands of pages of documents and I had formally interviewed 25 witnesses.''
The inquiry is expected to wrap up late this year..
Mr Habib returned briefly to Egypt this year, following the downfall of the Mubarak regime.
He is suing the former government for his torture, specifically naming the former head of intelligence, Egyptian Vice-President Omar Suleiman, and Gamal Mubarak, the son of the former president Hosni Mubarak.