The Syrian Observatory for Human Rights said 12,751 detainees in government detention centres had died from torture during the conflict.
"Some of the families of those killed under torture were forced to sign statements that their loved ones had been killed by rebel groups," said Observatory head Rami Abdel Rahman.
He told AFP that the toll did not include more than 20,000 detainees who have "disappeared" in government prisons and whose fate remains unknown.