Indian doctor Mohammed Haneef's almost four week-long ordeal neared its end on Saturday with the Australian government giving him the green light to leave the country after clearing him off terror charges, but refused to reinstate his work visa.

Haneef will fly out of Australia on Saturday night. His lawyer Peter Russo will fly to India with him, but said the fight to have Haneef's Australian work visa would continue.

The Gold Coast-based doctor was released from a Brisbane jail on Friday after a charge against him of providing support to a terrorist organisation was dropped.

Australian Immigration Minister Kevin Andrews, who cancelled Haneef's work visa on July 16 when a Brisbane magistrate granted the doctor bail, said the visa remained cancelled.

He said Haneef's lawyers had contacted the Immigration Department asking if the doctor could leave Australia as soon as possible.

"After taking advice, including from the Australian Federal Police, I have indicated that the Commonwealth has no objection to Dr Haneef leaving Australia. Indeed the effect of the visa cancellation is that he should remove himself, he should depart Australia in any event," he said.

Andrews said Haneef's Indian passport would be given back to him, although his visa remained cancelled.