The US department of defence was to release the images by May 28 in response to legal action filed by the American Civil Liberties Union (ACLU).
The photographs come from more than 60 criminal investigations between 2001-2006 and are of military personnel suspected of abusing detainees, officials said in April.
"The president does not believe that the strongest case regarding the release of these photos was presented to the court and that was a case based on his concern about what the release would do to our national security," Robert Gibbs, the White House press secretary, said on Wednesday.
The administration of George Bush, the previous US president, had argued against the release of the photos in part by saying it violated the privacy rights of the detainees and military personnel.
The ACLU was quick to condemn Obama's decision.
"The decision to not release the photographs makes a mockery of President Obama's promise of transparency and accountability,'' said Amrit Singh, an ACLU lawyer.
"It is essential that these photographs be released so that the public can examine for itself the full scale and scope of prisoner abuse that was conducted in its name."
Obama told his legal team last week that although he did not feel comfortable with the release of the photos, in no way did he excuse the behaviour of those responsible for tough interrogation tactics, a US official said.
The release of photos of abuse of Iraqi detainees at Abu Ghraib prison in Iraq in 2004 caused widespread anger.
The case could now be decided by the US supreme court.