Over the last five years, 700 goats have been tethered in decompression chambers and subjected to high pressure, causing extreme pain and the collapse of vital organs.
The experiments have been condemned as cruel and unnecessary by MPs who say data on the effects of deep diving have been known for years. Next week they will ask questions in the Commons about the experiments, and exactly how goats many have died.
The experiments are being done by the Defence Evaluation and Research Agency (Dera), testing treatments for men hurt escaping from submarines.
The tests are designed to see how much pressure a person can endure while trapped under the sea and the ability of humans to survive extreme forms of "the bends".
Sources at Dera say that when the experiments begin in the chambers the goats "bleat and leap around".
"Goats are being used as the experimental model for this programme because their physiological behaviour in these circumstances approximates very closely to that of humans," Sir John Chishulm, chief executive of Dera, said in a letter to Mike Hancock, Liberal Democrat MP for Portsmouth South. "The animals are not immersed in water but are subjected to varying levels of atmospheric pressure whilst in a pressure chamber. They are continuously monitored during the experiment." In 1998, 124 goats were used and since 1993, 699 goats have gone through tests. Some are put down and many are used more than once.
Conditions for animals in military experiments have been tightened under Labour and each new experiment must be licensed by the Home Office. There was a furore when the Independent on Sunday revealed the MoD was using live pigs to test ammunition.
"We only use animals when we are absolutely have to," said a spokeswoman for Dera. "We always try to limit the number of animals. Ideally, we would like not to use any."
Mr Hancock said: "They must be taking the goats to near- death. We can only deduce that these animals are suffering abysmal pain. Submarine technology has been with us for a long time. I cannot believe we still need to carry out these experiments."