The Obama administration announced last month it had agreed to release hundreds of photos from US-run prisons in Iraq and elsewhere in response to a long-running lawsuit by the American Civil Liberties Union.
The photos were used as evidence in criminal investigations of US soldiers accused of abusing detainees during president George W. Bush's administration.
Obama said issuing the photos would "inflame anti-American opinion and put our troops in greater danger" without shedding any new light on past abuses under the previous administration of George W. Bush.
He told reporters "that the publication of these photos would not add any additional benefits to our understanding of what was carried out in the past by a small number of individuals."
Obama said he was concerned that the images could have a "chilling effect" on future investigations into abuse.
But the president also said that "any abuse of detainees is unacceptable" and would not be tolerated.
The White House said the government would fight the release in court using a new legal argument on grounds that the photos would undermine national security.
The president "doesn't believe that the government made the strongest case possible to the court and asked the legal team to go make that case," White House spokesman Robert Gibbs said.
The Bush administration had argued against the release of the photos in part by saying it violated the privacy rights of the detainees under the Geneva Conventions.
The ACLU and other rights groups condemned Obama's decision as a betrayal of his promise to restore the country's moral reputation and break with his predecessor's secretive policies.
"The Obama administration’s adoption of the stonewalling tactics and opaque policies of the Bush administration flies in the face of the president’s stated desire to restore the rule of law, to revive our moral standing in the world and to lead a transparent government," Anthony Romero, executive director of the ACLU, said in a statement.
The photos are part of a wider debate about interrogation tactics against terror suspects employed by the Bush administration, with rights groups and Democratic lawmakers saying Bush-era figures approved torture.
Obama took the decision after weeks of discussions and amid growing anxiety within the administration about the possible effect of the photos in Iraq, Afghanistan and elsewhere, defense officials said.
As a May 28 deadline approached for the release of the photos under an agreement with the ACLU, "anxiety levels went up across the government" about the possible fallout from the images, Pentagon spokesman Bryan Whitman told reporters.
The commander of US forces in Iraq, General Ray Odierno, was an especially "passionate" opponent of releasing the photos and his views had an impact on Defense Secretary Robert Gates and other administration officials, Pentagon press secretary Geoff Morrell said.
Odierno, "was really the one who persuaded the secretary that this was something that had to be fought," Morrell told reporters.
Gates and other members of Obama's national security team argued against the release of the images, saying it could undermine US efforts in Afghanistan just as additional troops are deployed and before crucial elections in August, he said.
Officials concluded that "the timing was particularly bad in Afghanistan," he said.
Gates was among a number of officials who advised Obama to fight the release of the photos in court.
"I think he (president) heard from a lot of people the concerns of the commanders," Morrell said.
Lawyers for the Justice Department and Pentagon had previously concluded the administration's legal options had virtually run out but the administration may choose to appeal the case to the Supreme Court.
The case dates back to a Freedom of Information request in 2003.
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