The unit, called the Strategic Support Branch, has also been in operation in other places sources would not disclose, the Post said, citing documents and interviews with participants.
A early planning memorandum to Defense Secretary Donald Rumsfeld from the chairman of the Joint Chiefs of Staff, General Richard Myers, said the focus of the initiative was on "emerging target countries such as Somalia, Yemen, Indonesia, Philippines and Georgia," according to the Post.
The secret spying organization is designed to provide Rumsfeld with tools to conduct so-called human intelligence tasks, such as interrogation of prisoners and recruitment of foreign spies.
Recruited agents may include "notorious figures" whose association with the US government would be embarrassing if revealed, the Post said, citing a Pentagon memo.
Rumsfeld has been trying since October 2001 to provide the US military faster access to intelligence and new tools to penetrate terror groups such as Al-Qaeda.
But the Pentagon's initiative encroaches on the traditional territory of the CIA and gives Rumsfeld unprecedented authority over foreign spying at a time when Congress is trying to group an array of intelligence agencies under a new national intelligence director.
Rumsfeld for months opposed the creation of the new post and was instrumental in stalling passage of intelligence reform legislation recommended by the commission that investigated US intelligence failures prior to the September 11, 2001 attacks.