Animal Aid has accused scientists of conducting research programmes that were "frenzied and irrational".
A shocking film of publicly available footage showing how the rodents suffer was also released. Examples of alleged abuse included animals being poisoned with salt, injected with acid, forced to inhale tobacco smoke, and given electric shocks.
Animal Aid's investigation follows a dramatic increase in the use of GM mice in the last decade. Mice made up 71% of the record 3.79 million animal procedures started in British laboratories in 2011, according to the latest Home Office figures.
In 2011, almost two million procedures were started on mice whose genes had been changed, said the Animal Aid report, entitled Science Corrupted: The Nightmare World of GM Mice. These included GM mice and mice with harmful mutations induced by poisons or other external means. The number of procedures performed on mice in general had increased from 1.45 million in 1995 to nearly 2.68 million in 2011. Genetically altered mice accounted for 70% of the 2011 total.
Animal Aid director Andrew Tyler said: "Science Corrupted lays bare for the first time the true scale and nature of the GM mouse revolution. It describes an enterprise that has turned into something frenzied, scientifically irrational and terrifyingly cruel.
"Until now, public discourse around the subject has been dominated by the soothing narrative of the practitioners. They claim that the GM mouse revolution is morally and medically justified. Our incisive and thoroughly researched report tells the real, appalling and macabre story."
Sharmila Nebhrajani, chief executive of the Association of Medical Research Charities, said: "Where possible, our researchers use cells grown in a lab, computer models and human volunteers. When this isn't possible, research may involve animals."
She added: "When researchers need to use animals, this is strictly regulated to ensure they do not suffer unnecessarily and we strive to reduce the number needed, and seek to develop viable alternatives. Without this research, we cannot hope to find effective treatments for conditions which continue to affect people's lives."
Scientific progress is possible without using or inflicting pain to other animals. Learn more > > animalequality.net/animal-experimentation