Australian government's decision to revoke Indian doctor Mohamed Haneef's visa does not override the decision of a magistrate to grant him bail, country's Immigration Minister Kevin Andrews said on Tuesday.

Defending Monday's decision to cancel Haneef's 457 temporary skills visa, Andrews said this has been done because he 'reasonably suspected' that Haneef had an association with people involved in terrorism.

On Monday, the minister intervened to keep Haneef behind bars just hours after he was granted bail by Brisbane Magistrates Court on a charge of recklessly providing support to terrorism.

However, Andrews said it cast no aspersion on Haneef's guilt or innocence.

'Nothing that I have done has said anything one way or the other about the innocence or the guilt to be determined by the court of Haneef,' he told Channel 7.

'What I have said, though, is that given the information that I have got and given my responsibility to the national security and the national interest, then I did not believe I had any other alternative but to remove his passport,' he added.

Haneef would receive a fair trial, Andrews said.

'There are trials that happen every day that the media have commented on. But those trials go ahead, and we have a system, and the judges of the courts in Australia are very good at ensuring a fair trial,' he said.

After being held in custody for almost two weeks under anti-terrorism laws, 27-year-old Haneef was charged on Saturday with 'recklessly' supporting a terrorist organisation, for providing a mobile phone SIM card to a relative involved in the failed UK car bomb attacks.

While Federal Labour has offered its support, critics like Greens leader Senator Bob Brown suspect there is a political motive lurking behind the minister's decision.

"The Howard government has always resorted to the fear factor, to the cost of somebody. It is very dangerous business when politicians start interfering with judiciary," he said, adding that revoking Haneef's visa is a case of guilt by association.

However, Andrews said the move to detain Haneef was not political, but a matter of national security.

"The evidence is sufficient that I take that serious act. I am acting in the national interest and about matters that go to national security."