Shocking images of inmates in Iraq are the kind of images whose release the president has now vowed to fight in court.
They risk provoking renewed hostility in the Middle East as Mr Obama attempts to build bridges with the Islamic world.
He is scheduled to make a major speech in Cairo on June 4 when he will launch his version of a plan to bring peace between the Israelis and the Palestinians.
One picture showed a prisoner hung up upside down while another showed a naked man smeared in excrement standing in a corridor with a guard standing menacingly in front of him. Another prisoner is handcuffed to the window frame of his cell with underpants pulled over his head.
Others yet to be released reportedly show military guards threatening to sexually assault a detainee with a broomstick and hooded prisoners on transport planes with Playboy magazines opened to pictures of nude women on their laps.
The images emerged from Australia where they were originally obtained by the channel SBS in 2006 in the wake of the Abu Ghraib scandal. They now believed to be among those the president is trying to block.
Mr Obama previously committed to allowing thousands of images to be published but changed his mind after senior generals warned that their publication could place US troops serving in Iraq and Afghanistan in greater danger.
The president's change of heart brought bitter criticism from the left wingers and the American Civil Liberties Union, which had brought a freedom of information case against the US government applying to see the pictures.
Pledging to fight the case all the way to the Supreme Court, the ACLU accused him of betraying his principles of open government and "complicity in covering up" the "commission of torture by the Bush administration".
"It is true that these photos would be disturbing. The day we are no longer disturbed by such repugnant acts would be a sad one," said Anthony Romero, executive director.
"Only by looking squarely in the mirror, acknowledging the crimes of the past and achieving accountability can we move forward and ensure that these atrocities are not repeated."
The White House legal team was yesterday preparing for a June 9 deadline to present its case that it would be against the interests of national security to make the pictures public.
The controversy came as it was revealed that the administration is considering detaining terror suspects from Guantanamo Bay indefinitely and without trial on US soil.
Lindsey Graham, a Republican senator, said after meeting White House lawyers that terror suspects deemed too dangerous to release could be jailed permanently by a new national security court.
Other options include revising the Bush administration's military commissions for senior al-Qaeda suspects that have been criticised for relying too heavily on hearsay and uncontestable intelligence information.
When he took office on Jan 20 Mr Obama ordered that the prison at a US naval base on Cuba be closed within a year.
