The jury failed to reach a verdict for a second day and will continue deliberations on Wednesday.
The possibility of a mistrial was raised on Tuesday after prosecutors said the judge gave flawed instructions to a jury of military officers and asked him to revise it.
Military prosecutors asked the judge to revise the instructions he gave on what constitutes a war crime to the jurors.
Defence lawyers said the instructions were correct but argued that if the judge found otherwise a mistrial should be declared, as changing instructions after deliberations began would be extremely prejudicial to Hamdan.
|Hundreds of prisoners remain at the Guantanamo Bay prison [GALLO/GETTY]
However, the judge ruled that although the instructions may have been erroneous the prosecution had in effect waived their right to challenge them as they had not raised the issue sooner.
The military jury must reach a majority verdict in order for it to be considered valid.
Even if found innocent, Hamdan might not be freed, since the US military reserves the right to indefinitely hold "enemy combatants".
Despite the mistrial concerns on Tuesday, Geoff Morrell, a Pentagon spokesman, said the trial was "a good first effort" and said the US felt it had been "a fair and transparent process".
Prosecutors allege Hamdan was trained to use weapons at an al-Qaeda camp and also "delivered weapons, ammunition or other supplies to al-Qaeda members and associates".
"Hamdan was al-Qaeda, every fact in this case points to that," said John Murphy, a US prosecutor, in closing arguments on Monday, describing Hamdan as an "al-Qaeda warrior".
But Lieutenant Commander Brian Mizer, an assigned military defence lawyer for Hamdan, told the court that "this is a classic case of guilt by association".
"Mr Hamdan is not an al-Qaeda warrior, he is not al-Qaeda's last line of defence," Mizer said.
"He's not even an al-Qaeda member."
Hamdan is the first to undergo a full trial at the Guantanamo Bay prison camp and the case is an important test of the military commission system set up as part of the Bush administration's "war on terror".
The Yemeni national was captured at a roadblock in southern Afghanistan in November 2001, allegedly with two surface-to-air missiles in his car.
He says he drove for bin Laden in Afghanistan because he needed the $200 in monthly wages but denies joining al-Qaeda, pledging loyalty to bin Laden or participating in attacks.
Hamdan has already spent six years in prison at the Guantanamo prison camp, and his defence lawyers say he was subjected to abuse while in US custody, including humiliating interrogation tactics and sleep deprivation.
The Bush administration has faced heated criticism over the Guantanamo Bay prison camp and the special tribunals, which operate under different rules to other military courts or civilian ones.
Only a small group of authorised observers and journalists are allowed into the small courtroom and military authorities prohibit television news networks from recording the proceedings.