The president has faced strong opposition from legislators, including from his own Democratic party, to the transfer of prisoners to US soil for detention and trial.
Nick Spicer, Al Jazeera's correspondent in Washington, said the delay in the Guantanamo review report was not unexpected.
"It certainly is a measure of the obstacles that the [Obama] administration has been facing, the biggest of which was when the congress refused to give the funding needed to shut the prison at Guantanamo Bay [in May]," he said.
"With the six-month extension, what we can now expect is for the men and women writing it - who are from the government, lawyers, from the military and so on - will be consulting more closely with the US congress to widen the number of players involved in the closure of Guantanamo Bay."
A separate government task force reviewing rules for the interrogation of detainees also fell short of its Tuesday deadline and has been granted an extra two months to submit a final report, senior administration officials said.
But the panel on detentions did issue a five-page interim report late on Monday that said "where appropriate, prosecution of those responsible must occur as soon as possible, whether in federal court or before a military commission".
"Justice cannot be done, however, unless those who are accused of crimes are proved guilty beyond a reasonable doubt in a court of law that affords them a full and fair opportunity to contest the charges against them," it said.
Obama has ordered that the Guantanamo prison be closed by January 2010 but, six months on, fewer than 20 detainees have been transferred and 229 remain in the jail.
|Obama's order to close Guantanamo has faced congressional opposition [AFP]
A senior administration official has said the justice department is considering prosecuting about 30 others in federal courts, and another 30 or so could face trial by military commissions.
Ramzi Kassem, a lawyer for three men held at Guantanamo, said the delay of the reports on Guantanamo was due to fighting within the Obama administration.
"As a first step, the Obama administration should have taken in Guantanamo detainees [into the US] and that would have encouraged other countries [to take detainees].
"As a second point, the administration could have done a better job of explaining to the US public who exactly was held at Guantanamo and making clear that the men at Guantanamo are not the worst of the worst.
"Maybe as a third step, the Obama administration could have reached past European countries and looked for other countries who would be willing to take in Guantanamo detainees."
Government lawyers have so far finished the reviews of more than half of the detainees and more than 50 suspects are believed to have been cleared for transfer to other countries.
Some of the detainees will be held indefinitely without charge, subject to occasional judicial review, the Obama administration has said.
'Great legal mess'
Sahr Muhammed Ally, a lawyer who works on US counter-terrorism and national security policies, told Al Jazeera that Guantanamo was a "great legal mess" that the Bush administration left for the Obama administration.
"We have made several recommendations to the [Obama] administration that individuals being held in Guantanamo be prosecuted in civilian federal courts in the US, but we have heard they are doing a case-by-case analysis on each prisoner to see whether [this can happen]," she said.
"It doesn't help that congress is blocking funding to transfer any individuals from Guantanamo to the US mainland."