Wikileaks sparked controversy last month when it published more than 70,000 military documents relating to the war that revealed an unvarnished, and at times disturbing picture of the conflict.
The Pentagon said that the leak - the largest in military history- had put US troops and Afghan informers in danger. Morrell warned that more publications would cause further damage.
A Pentagon task force of around 80 people is combing through the materials already posted on the website and flagging up documents deemed to pose a risk. Morrell said that foreign governments were being notified of dangerous material.
The analysts have already carried out about 400 initial 'word searches' of the leaked documents and are continuing to work around the clock to carry out a more detailed study of what exactly has found its way into the public domain.
The Pentagon has some idea of the material that Wikileaks is holding back and is working to pre-empt the possible release of the documents, Morrell said.
Morrell refused to comment on potential legal action against Wikileaks, saying it was a matter for the FBI and US justice department to decide how to proceed.
But he said that the website was responsible for "brazen solicitation to US government officials, including our military, to break the law."
"WikiLeaks' assertion that submitting confidential material to WikiLeaks is safe, easy and protected by law is materially false and misleading'' he said.
The US investigation into the leaks is focused on Bradley Manning, an army intelligence analyst in Iraq who has already been charged with leaking a classified video showing a 2007 helicopter attack that left 12 people, including two Reuters journalists, dead in Baghdad.
Meanwhile, Wikileaks has posted a huge encrypted file named "Insurance" to its website, sparking speculation that the organisation may be threatening to publish more classified information if its staff are detained or the website is attacked.