In a submission to the Clarke inquiry into the case, the department offered no support for the decision, saying it had provided Mr Andrews with a range of options for dealing with the doctor falsely accused of supporting a British terrorism plot.

The department was "confident all its officers acted appropriately in the handling of the case and in providing advice to the former minister", the submission said.

The 23-page document twice described its approach to the case as a "whole of government" process.

On July 16 last year Mr Andrews cancelled the 457 visa that permitted Dr Haneef to live and work in Australia. The power to cancel a visa on character and national interest grounds is typically employed as a last resort measure, but in this case was employed less than three hours after a Brisbane court granted the Gold Coast doctor bail. The rationale by which Mr Andrews decided Dr Haneef failed a character test has not been explained. It was protected from disclosure in the submission yesterday because the information was sourced from an intelligence or law enforcement agency, the report said.

Dr Haneef was arrested at Brisbane International Airport on July 2. Police charged him with recklessly providing resources to a terrorist organisation, alleging his mobile phone SIM card had been found in the wreck of a car driven into a Glasgow airport terminal the month before. This was later proved to be false. "What is very important is the timeline," Dr Haneef's lawyer, Rod Hodgson, said yesterday.

"The department had started to consider a plan involving immigration laws within 24 hours of Dr Haneef being detained on a criminal matter."

On Saturday, Mr Hodgson said Australian Federal Police may have broken the law by withholding five transcripts of early interviews conducted with Dr Haneef for more than a year. In these interviews, Dr Haneef had defended himself against police suspicions of involvement in a terrorist plot, Mr Hodgson said. The doctor had explained he would be coming back to Australia and was flying to India on a one-way ticket, purchased by his father-in-law, to see his wife and newborn baby.

His three requests for a lawyer, an obligation by law, had also been ignored, Mr Hodgson said.

The case against Dr Haneef collapsed on July 27 after the Commonwealth Director of Public Prosecutions dropped the charge, saying a mistake had been made. By then, Dr Haneef had been detained for 25 days. The day after charges were dropped, the department's attitude changed. It provided a decoy to divert media away from the correctional centre where Dr Haneef was being held so he could be moved into a Brisbane apartment.

The department's Brisbane office paid for Dr Haneef's passage to India. "[The department's] Brisbane office assisted Dr Haneef to purchase clothes, and paid for an economy airline ticket to India for him, his cousin and his lawyer," the submission said.