A probe has been launched to find out how security was breached at the heavily guarded Bagram base, which co-ordinates the fight against the Taliban and al-Qaeda and hosts one the US army's main detention facilities.
Shopkeepers said the flash drives were stolen by some of the 2,000 Afghans employed as cleaners, office staff and labourers at Bagram.
Although workers are searched going in and out of the base, the drives are the size of a finger and can easily be concealed on a body
Names of spies
The Los Angeles Times reported on Friday that maps, charts and intelligence reports on the computer drives "appear to detail how Taliban and al-Qaeda leaders have been using southwestern Pakistan as a key planning and training base for attacks in Afghanistan".
It said the drives also "appear to contain the identities of Afghan sources spying for US Special Forces that operate out of the Bagram base".
They also contain assessments of targets, descriptions of US bases and their defences in Afghanistan and plans to remove or marginalise problematic Afghan officials.
The paper quoted an army spokesman as saying that "we're obviously concerned that certain sources or assets have been compromised".
An Associated Press reporter was able to review about 40 of the drives for sale on a laptop computer
Most were blank or did not work, but three contained data, including a soldier's military discharge certificate, troop resumes and photographs of Air Force One during a visit to Afghanistan last month by George Bush, the US president.
Other memory drives viewed during the week contained the social security numbers of hundreds of soldiers, including four generals, and lists of troops who completed nuclear, chemical and biological warfare training.
Money no object
The social security numbers of US generals and a list of military spies were leaked after the theft five days ago - although the accuracy of the data could not be verified.
Dozens of stolen memory sticks were still on sale at the market just outside the base on Friday.
A local shopkeeper, who spoke on condition of anonymity, said US soldiers went around the market on Thursday carrying "a box full of afghanis (the Afghan currency), buying all they could find".
"They said they wanted them all and price wasn't important."