Khadr, who is charged with the killing of a US soldier in Afghanistan, was only 15 when he was captured in the country in 2002 and sent to the facility.
The son of a now dead suspected funder of the al-Qaeda network, Khadr faces a maximum life sentence if convicted.
The news comes as a federal judge ordered the US government to publicly reveal unclassified versions of its allegations and evidence justifying the ongoing detention of around 100 detainees still being held at Guantanamo Bay.
The Justice Department had been filing unclassified versions of its legal documents under seal, so that they could only be seen by judges, lawyers and government officials, citing security reasons.
However US district judge Thomas Hogan agreed with detainees' lawyers and the US media, who had argued that the public has a right to access the records.
Obama sparked criticism last month when he said he would retain the special military trials, a system devised by George Bush, his predecessor.
|Uncertainty remains over the fate of those
held at Guantanamo Bay [AFP]
However, he said the trials would proceed with some changes, such as banning the use of evidence obtained through coercion, limiting hearsay evidence and granting detainees the right to choose their lawyers.
Al Jazeera's Monica Villamizar, reporting from Guantanamo Bay, said that the uncertainty over Khadr's case showed how difficult and slow efforts to try those remaining at the facility were going to be despite the modifications.
The judge was also due to address a request from Obama for a new 120-day suspension of all pending commissions cases, that would keep them on hold until mid-September.
The US president wants the time to review strategy for prosecuting those detained and to introduce the system changes, which he says will give detainees stronger legal protections.
So far, judges have agreed to the extension for nine of the 11 detainees facing charges at Guantanamo.
In another development on Monday, 17 Uighurs detainees held at Guantanamo sent a letter to Obama demanding their release, our correspondent said.
|About 240 detainees continue to be held at the Guantanamo Bay prison [EPA]
Their appeal came four years after the men - members of a largely Muslim group in northwestern China - were cleared for release from the camp.
However, they remain at Guantanamo Bay because the state department fears they will face persecution if returned to China.
He has faced congressional opposition in getting an $80m budget approved to decommission the prison by January 2010 and move the remaining inmates.
Obama said he wants to close the prison at Guantanamo Bay by January next year, but officials say he will probably need to extend this deadline or move the trials elsewhere.
US legislators say they want a detailed outline on the fate of the 240 detainees once the prison is closed, as communities across the country oppose the prospect of moving them to US soil.
The president has since firmly defended his decision to close Guantanamo saying it was a move to clean up "something that is quite simply a mess", referring to efforts to reverse his predecessor's policies.