David Hicks is accused of conspiracy to commit war crimes, attempted murder and aiding the enemy, the Pentagon said on Thursday.
However, the lawyer appointed by the military to defend Hicks is promising to fight US claims.
"The defence team intends to fight these allegations - and that's all they are is allegations - to the fullest extent that we're allowed to, and the resources that are provided to us," said military lawyer Marine Corporal Major Michael Mori.
Hicks, captured in Afghanistan in late 2001, will face trial before a US military tribunal, although no date has been set, the Pentagon said in a statement.
While the United States holds about 600 non-US citizens at the US naval base at Guantanamo Bay, Cuba, Hicks, 28, became just the third Guantanamo prisoner to be charged with a crime. Another Australian citizen, Egyptian-born Mamdouh Habib, is being held there without charges.
The military tribunals, formally called commissions, will be the first of their kind for the US since World War Two. The Pentagon confirmed earlier statements by the Australian government that US prosecutors will not seek the death penalty against Hicks.
"It's unfortunate these allegations will never be tested in a fair and established justice system. It's such a departure from fundamental fairness"
Corporal Major Michael Mori,
military lawyer to Hicks
Human rights and legal activists have criticised the US for holding prisoners in Guantanamo without charges, while excoriating the rules established for the military tribunal trials as rigged to yield convictions.
Military lawyers assigned by the Pentagon to defend Guantanamo prisoners have been among the most critical.
'No independent judiciary'
"It's unfortunate these allegations will never be tested in a fair and established justice system. There's just a complete lack of the independent judiciary and the independent appeals process that are the backbone of any criminal justice system we're used to. It's such a departure from fundamental fairness," Mori told Reuters.
The Pentagon statement said "military commission procedures provide for a full and fair trial," including the presumption of innocence, a requirement of proof beyond a reasonable doubt
to secure a conviction and an opportunity to present evidence and call witnesses.
Rights groups have criticised
holding detainees without charge
But critics have noted the entire process is controlled by the Defence Department, including the appointment of the panel that will hear the case and a review panel to which any appeal would go. Unlike normal US military courts, there is no right to appeal to a civilian court in the military commissions.
Two months after the 11 September attacks, President George Bush authorised military trials of non-US citizens caught in what he calls the global war on terrorism.
Held for two years
Hicks was held at Guantanamo for more than two years before being charged with conspiracy to commit war crimes, attempted murder by an unprivileged belligerent and aiding the enemy.
The Pentagon alleges Hicks attended al-Qaida training camps in Afghanistan and allegedlu conducted surveillance of the US and British embassies in Kabul.
Prosecutors allege Hicks travelled to Afghanistan in January 2001 to attend a variety of al-Qaida training camps after allegedly joining a paramilitary organisation fighting for Albanian Muslims in Kosovo and an Islamist group in Pakistan.
Prosecutors also allege Hicks met with al-Qaida leaders including Usama bin Laden and Muhammad Ataf, and performed tasks including translating al-Qaida training materials from Arabic to English.
In February, the Pentagon charged Ali Hamza Ahmad Sulayman al Bahlul of Yemen and Ibrahim Ahmad Mahmoud al Qosi of Sudan.
Earlier, the Australian government called on the US to lift a confidentiality agreement signed by Hicks' lawyers after claims that he and Habib were abused and tortured at Guantanamo.
Bush promised a full investigation
into abuse claims at Guantanamo
Australia has also asked for a psychological exam for Habib, who allegedly became mentally unbalanced after US guards falsely told him that his wife and children had died.
The abuse allegations prompted US President George Bush to promise Australian Prime Minister John Howard a full investigation into the conditions of the two Australians.
"The military is fully investigating any allegations as to whether or not they've been mistreated," Bush told reporters at a news conference with Howard on 3 June.