The list includes the names of four people considered for the first time as missing. In total, it provides details of 39 people from Egypt, Kenya, Libya, Morocco, Pakistan and Spain.
"'Off the Record' highlights aspects of the CIA detention programme that the US government has actively tried to conceal, such as the locations where prisoners may have been held, the mistreatment they endured, and the countries to which they may have been transferred," a statement from the groups said.
George Bush, the US president, admitted to the existence of the secret prisons programme in September, but his administration insisted that after the transfer of 14 prisoners suspected of being involved with al-Qaeda to the US naval facility in Guantanamo Bay, Cuba, the CIA would no longer have any prisoners in its custody.
The report also says that family members of those detained in the secret prisons, including their spouses and children as young as seven, were also detained in secret.
They cite the example of Khalid Sheikh Mohammad, thought to be the leader of the group responsible for the September 11, 2001 terrorist attacks on the United States, whose children, aged seven and nine, were arrested in September 2002.
"According to eyewitnesses, the two were held in an adult detention centre for at least four months while US agents questioned the children about their father's whereabouts," the organisations say.
"The duty of governments to protect people from acts of terrorism is not in question," said Claudio Cordone, senior director for research at Amnesty International.
"But seizing men, women and even children, and placing people in secret locations deprived of the most basic safeguards for any detainees most definitely is. The US administration must end this illegal and morally repugnant practice once and for all."
Amnesty, the CCR and the International Human Rights Clinic of New York University School of Law also announced on Thursday that they had filed a lawsuit in a US federal court seeking the disclosure of details regarding the prisoners they allege are still being held in secret, under freedom of information laws.
The existence of secret prisons run by the CIA, revealed in 2005 by the Washington Post, has sparked strong emotions around the world, particularly in Europe, where two inquiries have shown that several countries co-operated with the programme.