Under the new system, the charges filed by the prosecutor, Colonel Moe Davis, now have to be reviewed by other officials before the men can be formally charged.
David Hicks, an Australian, was arrested in Afghanistan in late 2001 and has been accused of fighting for al-Qaeda and conducting surveillance of US and British embassies on its behalf.
The prosecutor filed charges against Hicks, 31, of providing material support for terrorism and attempted murder in violation of the law of war, the Pentagon said.
Major Michael Mori, Hicks' military defence lawyer, criticised the charges saying even the prosecutor had stated that there was no evidence the Australian had shot at anyone in Afghanistan.
"The charge of material support is not part of the law of war and does not appear in any US or Australian military manual as a law of war offence."
John Howard, the Australian prime minister, had demanded charges be filed against Hicks by the end of February.
"I'm glad that the charges are being laid and that the deadline I set has been met," Howard said in Sydney on Saturday.
"They are very serious charges and that is why they should be dealt with as soon as possible."
Terry Hicks, David Hicks' father, said, "I would be more relieved if David was facing a fair and just situation, not virtually the same thing that they went through before, which has been ruled as illegal."
Bin Laden allegation
Hamdan is accused by prosecutors of acting as Osama bin Laden's driver and of transporting weapons for al-Qaeda. The charges filed against him are conspiracy and providing material support for terrorism.
Khadr is accused of murdering one US soldier with a grenade and wounding another during a firefight at a suspected al-Qaeda compound in Afghanistan. He was 15 when captured during the clash.
The prosecutor filed charges accusing him of murder in violation of the law of war, attempted murder in violation of the law of war, spying, conspiracy and providing material support to terrorism, the US defence department said.
|Protests for the closure of Guantanamo took |
place around the world in January [EPA]
The US Supreme Court ruled in 2004 that detainees could go to US courts to seek their release or changes in confinement conditions.
But in October 2006 George Bush, the US president, signed a law taking away prisoners' rights to the US court system.
Indonesia, however, has been allowed to interrogate an alleged terrorist chief held at Guantanamo, a police spokesman said.
US officials had previously refused Indonesian investigators access to Hambali, also known as Riduan Ismaddin, because they said doing so could compromise their own investigation of his activities.
General Sutanto, Indonesian police chief, said: "We need to question him to get more information on the [al-Qaeda] network in Indonesia."
Hambali, an Indonesian citizen, was arrested in 2003 by US Central Intelligence Agency operatives in Thailand.
He is alleged to be the operations chief of the al-Qaeda-linked group Jemaah Islamiyah, blamed for bombings in Indonesia, including the 2002 attack on the resort island of Bali which killed 202 people.
Indonesia has long demanded access to Hambali, who allegedly had links to two of the September 11 hijackers. He was also reported to be suspected of being involved in a plan to recruit new pilots for another wave of suicide hijackings in the US.
Washington says it plans to put him on trial, but he has not been charged with any crime.
More than 770 prisoners have been imprisoned at Guantanamo since the US began using the base to hold suspects captured during the so-called "war on terror" that Bush launched after the September 11 attacks.