Mohamed Haneef "has been charged with providing support to a terrorist organisation", said an Australian police spokesman.
Dr Haneef was stopped at Brisbane airport on 2 July, as he tried to leave Australia for India.
The inquiry is linked to the suspected attempted car bombings in central London and Glasgow last month.
Dr Haneef is being charged with providing a mobile phone SIM card to his second cousins, Sabeel and Kafeel Ahmed, both of whom are being held in Britain.
The BBC's Nick Bryant in Brisbane says the charges carry a maximum sentence of 25 years in jail.
Dr Haneef is due to appear in court in Brisbane later on Saturday. His lawyer is in the process of applying for bail.
He is one of eight people who have been detained over the alleged attacks. The others - all linked to the medical profession - were picked up in the UK.
Dr Haneef came to Australia in September last year and worked as a registrar at a hospital on Queensland's Gold Coast.
Before that he had worked in the National Health Service in Britain.
A major investigation has been under way in the UK since two cars containing petrol, gas cylinders and nails were discovered in central London on 29 June. They failed to explode.
One day later, a burning car loaded with gas cylinders was driven into the main terminal building at Glasgow's international airport. Two men were arrested at the scene and are now in custody.
Güncelleme Tarihi: 14 Temmuz 2007, 03:31