Pentagon spokesman Geoff Morrell said the Defense Department "demands that Wikileaks return immediately to the US government all versions of documents obtained directly or indirectly" from Pentagon databases or records.
The website's disclosure "of a large number of our documents has already threatened the safety of our troops, our allies and Afghan citizens who are working with us to help bring about peace and stability in that part of the world," he said.
"The only acceptable course is for Wikileaks to take steps immediately to return all versions of all of these documents to the US government and permanently delete them from its website, computers and records."
WikiLeaks is believed to have released some 92,000 classified documents on Afghanistan.
(Read: WikiLeaks-Reports from the ground in Afghanistan)
Morrell said that any additional public disclosure of classified information "can only make the damage worse."
The documents also included some names of Afghan informants.
WikiLeaks founder Julian Assange, 39, an Australian former hacker and computer programmer, said he believed publication would help focus public debate on the war in Afghanistan and on possible atrocities by US-led forces. (Watch: Assange to NDTV- ISI danger is very real)
The FBI and Pentagon are investigating the case and have been questioning a US soldier who has been charged with giving WikiLeaks classified video showing a July 2007 US Apache helicopter strike in Baghdad that killed several people.
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