More than six million animals including baboons, dogs, cats and native mammals are being used every year in Australia for medical research, experiments and surgical skills training, according to official figures.

Government statistics reveal that the biggest number of animals used was mice, with more than more than a million subjected to tests and experiments. Nearly 6000 dogs and more than 1500 cats were also used and a NSW government report showed that some exotic zoo animals had been the subject of experiments that involved "minor pain".

New South Wales was reportedly the biggest user of animals in experiments and surgery training with a total number of 2,699,532, with Victoria the second highest with 1,084,507 animals according to the statistics compiled by Humane Research Australia from state government resources.

Some states including Queensland have stopped revealing the number of animals used. The last figure that has been made available was in 2009. An average of previous years showed that approximately 1,202,343 animals had been used.

Nationally, there were 123,975 animals used in the "major physiological challenge" an official NSW category of experimental research, which means the animals remain conscious for some or all of the procedure "... which causes moderate or large degree of pain/distress, which is not quickly or effectively alleviated".

The revelations about the number of animals being used follows disclosures in Fairfax Media last week that baboons were being bred in Sydney and Melbourne and used in experiments including the transplantation of a pig's kidney into a baboon's body. The baboon named Conan had to be killed after suffering fatal side effects.

Not all the animals used experience pain and suffering. Some are just held for observation with "minor interference".

But there were more than 25,000 animals subject to an experiment with "death as an endpoint", in which the animal is suffering and the death of the animal is planned but the animal is not euthanised.

Helen Marston, the chief executive of Humane Research Australia, said that Australia was the fourth highest user of animals in experiments and surgery training in the world after China, Japan and the US.

Ms Marston said there has been a resistance to move away from the use of animals despite available alternatives that are being used around the world.

Dr Denise Russell, a research fellow at the University of Wollongong specialising in animals and ethics, said there is a lack of ethical scrutiny of the experimental projects.

"The ethical scrutiny for research comes at the end of a long process of grant application and approval. There is then an incentive for the animal ethics committees to simply accept the proposals. (If they don't institutions are denied that funding.) The scientists on animal ethics committees are required to be from areas using animal research and can't be expected to have good knowledge of alternatives," she said.

Dr Russell said most of the experiments done are not to get a cure for human disease.

"There's often hype about a new drug then nothing eventuates. All this suggests we are looking in the wrong place and alternatives should be investigated. Also the fact that there is poor transferability from animal to human studies suggests using animals to find out about humans is misguided."

The National Health and Medical Research Council (NHMRC) is responsible for funding research involving animals. It is currently reviewing its policy on the care and use of non-human primates for scientific purposes.

Professor Anne Kelso, the chief executive of NHMRC, was unavailable to answer questions from Fairfax Media but told the ABC last week that despite enormous advances in recent years "we are not yet at a point where all medical research can be done entirely outside an animal".

Professor Kelso said researchers were like the rest of the population and did not want to use animals unless there was strong justification. She said many people in Australia are working towards better models and some of the most advanced research in this area is being done in Australia.

Animals are still being used for surgical skills training despite alternatives such as mannequins and simulated skin being available.

Three states and territories, Victoria, Northern Territory and Tasmania this year have not scheduled surgical training with live animals. But NSW, Western Australia, and South Australia have scheduled surgical skills training for this year on live animals that will be killed afterwards.

Professor David Watters president of the the Royal Australasian College of Surgeons said in a letter to the Humane Research Australia they provided mannequins at three venues for the "small number of conscientious objections to using animals ... and to provide the opportunity to evaluate alternative simulation models as they become available".

Associate Professor Stephen Tobin, the Dean of Education at the Royal Australasian College of Surgeons in Melbourne said sheep and pigs were still used in some surgery while properly anaesthetised. Professor Tobin said there was constant review of surgical training experiences and that with the technological advances being made that the college may end up in the future with a non-animal situation.