In its Friday edition, the newspaper said the covert jail was set up to house valuable al-Qaida suspects.
Citing military officials and current and former intelligence officers, the newspaper said the CIA facility was built over the past year within a larger complex at Camp Delta where the defence department houses high-value detainees and those awaiting military trials.
Officials said the CIA buildings were shrouded by high fences covered with thick green mesh plastic and ringed with floodlights, according to the report.
The Post said it was unclear whether the CIA facility was still in operation. But it cited sources as saying that detainees from Pakistan, West Africa, Yemen and other countries have been housed there under the strictest secrecy.
An unidentified US official who visited the base in recent months was quoted as saying: "People are constantly leaving and coming."
Moazzam Begg may be one of
those held in the secret facility
Officials for the CIA and the Pentagon were not immediately available for comment.
The US military is holding at Guantanamo more than 500 people detained during its invasion of Afghanistan where it deposed the ruling Taliban.
The CIA is believed to be holding about three dozen suspected al-Qaida leaders in undisclosed locations, the Post said, quoting US national security officials.
The report said current and former US intelligence officials say the agency holds the most valuable suspected al-Qaida leaders and many mid-level members with knowledge of the group's logistics, financing and regional operations.