"These photographs provide visual proof that prisoner abuse by US personnel was not aberrational but widespread," said Amrit Singh, an ACLU lawyer.
The administration of George Bush, the previous US president, had argued that cases of abuse, such as that at Abu Ghraib jail in Iraq, were isolated incidents.
And the Pentagon said the images proved that its investigations into abuse allegations were serious.
"What this demonstrates is that we have always been serious about investigating credible allegations of abuse," Bryan Whitman, a Pentagon spokesman, said.
|Barack Obama has come under pressure after
a series of new revelations [AFP]
The case dates back to a Freedom of Information request made in 2003 by the ACLU.
After a federal appeals court ruled against the government last year, officials decided against an appeal to the US supreme court and to release the images.
"We felt this case had pretty much run its course," he said.
"Legal options at this point had become pretty limited."
Whitman said the Pentagon would release 44 photos already identified in the court battle with the ACLU, along with a substantial number of others.
The images are the latest in a series of revelations about the treatment of prisoners during the Bush administrations "war on terror".
Last week, Barack Obama, the US president, released memos that justified the use of torture by the CIA, a move that has sparked a wave of controversy in the US over the use of torture on detainees.
Obama said that CIA officers involved in interrogations should not be prosecuted as they were acting on orders but he has left the door open to possible prosecution of others involved in the writing of the memos.
The memo release was followed by two US senate reports, one of which said that Condoleezza Rice, the former US national security advisor and secretary of state, approved the use of torture methods such as waterboarding as before legal memos backing its use were written.