Clive Stafford Smith, a lawyer and legal director of Reprieve, an organization which represents several detainees at Guantanamo Bay, said: "We call upon the German government to order an independent investigation."
The organization said it believed Ramstein Air Base was used, though it added that it could have been another US Air Force base in Germany.
Reprieve cited information from three Guantanamo detainees, Hassan bin Attash, Binyam Mohamed and Shaker Aamer, in its report.
Attash was transferred to Jordanian custody in 2002 for 16 months after being arrested in Pakistan.
According to Reprieve, Attash claims he was told by his Jordanian torturers that his brother was being held for interrogation at a US prison at an air force base in Germany.
The brother, Waleed Tawfiq bin Attash, is an alleged senior al-Qaeda figure. On September 6, George Bush, the US president, announced Attash had been transferred to Guantanamo along with 13 other detainees who had been held by the CIA at secret locations.
"It has become clear that there is nothing to these accusations, there were and are no such facilities in Germany"
Thomas Steg, German government spokesman
Mohamed, who was held in Morocco for 18 months after being captured in April 2002 in Pakistan, says he was told by his Moroccan interrogators that Khalid Sheikh Mohamed was being held at a US prison in Germany, Reprieve said.
Aamer, who was also detained in Pakistan, believes that he and 30 other prisoners stopped in Germany and changed planes while being transported from Afghanistan to Guantanamo Bay in February 2002.
Reprieve said: "The prisoners were blindfolded and shackled, but Shaker Aamer could see underneath his blindfold and hear people talking."
Thomas Steg, a German government spokesman, rejected the accusations, saying officials already reported "comprehensively" to a secretive parliamentary panel.
He said: "It has become clear that there is nothing to these accusations, there were and are no such facilities in Germany."
The German government reported to the parliamentary investigating panel in February after allegations that CIA flights carrying prisoners passed through Germany.
John Pike, director of GlobalSecurity.org, a Washington-based military policy think tank, said it appeared plausible that Ramstein was used as a refuelling stop for CIA planes carrying detainees.
But Pike said it did not seem plausible that Ramstein housed a secret detention facility.
He said: "There are too many people there.
"It seems to me it would be noticed, an item of conversation."
Pike also questioned why interrogators in Morocco and Jordan would offer such information.
"I don't know what incentive an interrogator might have to provide such sensitive information.
"They're there to extract information, rather than to impart it."
Steg said US bases in Germany were "not a lawless zone" but did not explain whether the US military was obliged to inform German authorities about what went on there.