At least one picture shows an American soldier raping a female prisoner while another is said to show a male translator raping a male detainee, reports The Telegraph.
Further photographs are said to depict sexual assaults on prisoners with objects including a truncheon, wire and a phosphorescent tube. Another apparently shows a female prisoner having her clothing forcibly removed to expose her breasts.
Detail of the content emerged from Major General Antonio Taguba, the former army officer who conducted an inquiry into the Abu Ghraib jail in Iraq.
Allegations of rape and abuse were included in his 2004 report but the fact there were photographs was never revealed. He has now confirmed their existence in an interview with the Daily Telegraph.
The graphic nature of some of the images may explain Obama's attempts to block the release of an estimated 2,000 photographs from prisons in Iraq and Afghanistan despite an earlier promise to allow them to be published.
Major General Taguba, who retired in Jan 2007, said he supported the President's decision, adding: "These pictures show torture, abuse, rape and every indecency.
"I am not sure what purpose their release would serve other than a legal one and the consequence would be to imperil our troops, the only protectors of our foreign policy, when we most need them, and British troops who are trying to build security in Afghanistan. The mere description of these pictures is horrendous enough, take my word for it," he added.
The latest photographs relate to 400 cases of alleged abuse between 2001 and 2005 in Abu Ghraib and six other prisons. Mr Obama said the individuals involved had been "identified, and appropriate actions" taken.