Live pigs were blasted with explosives and forced to inhale mustard gas, and monkeys infected with anthrax during "disturbing and cruel" experiments at Porton Down, it was claimed.
Scientists at the top secret military research establishment in Wiltshire were accused of causing "substantial" suffering to animals in the past two years.
The alleged evidence was collected by the British Union for the Abolition of Vivisection (BUAV) from papers published in scientific journals.
In one study, reported in the Annals of Surgery in 2010, explosives were said to have been detonated eight feet from pigs that had been anaesthetised, wrapped in blankets, and placed on trolleys.
The animals were said to have suffered blast injuries and blood loss, after which an attempt was made to resuscitate them. Eleven out of 28 died, it was claimed.
Other pigs, which were eventually killed, suffered severe lung damage after inhaling phosgene and mustard gas, two lethal chemical weapons, according to the BUAV which added a number of experiments were funded by US defence agencies, or conducted in collaboration with them.
In a further experiment, funded by the US Defence Advanced Research Projects Agency (Darpa), marmosets were infected with anthrax before being treated with an antibiotic, it was alleged. Four animals died and those still alive at the end of the study were killed and dissected, it was claimed.
This study was published in the International Journal of Antimicrobial Agents last year. There were no reports of pain relief or other supportive measures and the monkeys must have "suffered immensely" before experiencing a painful death, said the agency.
Michelle Thew, chief executive of the BUAV, said: "Although supporting the need to ensure the safety of soldiers and civilians in an increasingly dangerous world, the BUAV is opposed to deliberately causing suffering and death to animals in such disturbing and cruel experiments. We believe it is totally unacceptable to treat animals in this way."
The Defence Science and Technology Laboratory (DSTL) based at Porton Down said: "The remit to provide safe and effective protective measures for the UK and its Armed Forces could not, currently, be achieved without the use of animals. DSTL operates in strict accordance with the Animals (Scientific Procedures) Act."