A string of baby baboons, just days old, suffered traumatic deaths after being torn in half or dying from wounds inflicted during fights among adult cage mates inside the secret baboon research colony on the outskirts of Sydney.

While at least a dozen babies have died from trauma, the majority of adult baboons at the Wallacia compound that had died in its first 24 years of operation were dying from something different – the spread of lymphoma – a wasting-related disease.

Fairfax Media has obtained two scientific research papers that have given the first public insight into the lives and health of the baboons, which are bred specifically for experiments and are kept far from the public gaze, in the semi-rural area of Wallacia. The research recorded 99 deaths, 42 of them accidental and mainly babies.

No details have ever been publicly revealed about the facility, overseen by the Royal Prince Alfred Hospital, nor the welfare of the baboons which have been used for medical experiments including xenotransplantation and for research into diseases in pregnancy including pre-eclampsia.

The research papers revealed the colony, which was started in 1982 using 30 baboons – 20 females and 10 males brought to Sydney from the Windsor Park Zoo in Britain. Three young adult males were also brought in from the Perth Zoo.

The research papers published in the Journal of Medical Primatology and the Australian Veterinary Association revealed for the first time details of what had been happening to the baboons inside the secret facility.

A primate expert who did not wish to be named said incidents such as the neonatal deaths are not uncommon in groups – usually at the height of stress or if the group is not strong. But she said the numbers would have to be compared with other similar groups in captivity for a meaningful analysis. It is not known whether that was done.

Fairfax Media contacted the director of the Baboon facility, Professor Anne-Marie Hennessy, but she did not respond.

A spokeswoman for Sydney Local Health District said the care and wellbeing of the colony is the responsibility of a full-time veterinarian on site, its Animal Ethics Committee, the Animal Research Review Panel of NSW and representatives from the National Health and Medical Research Committee.

She said the husbandry, monitoring, breeding and use in research of the animals complies with all relevant legislation. She said that information on the cases was published and made available to all appropriate authorities.

"Routine screening of the colony conducted within the past 20 years detected a small number of primates with lymphoma, a non-contagious form of leukaemia," said the spokeswoman.

"Lymphoma in primate colonies is not unusual. Primates are subject to cancers in the same way as humans, and develop them both in the wild and in captivity. Information on the cases was published and made available to all appropriate authorities. There have been no ongoing issues with lymphoma in the colony."

The department did not answer questions about how many baboons had died from lymphoma and whether the number had gone up or down since the report was published.

The research obtained by Fairfax Media shows there were 57 deaths from illness and disease in the study period from 1982 to 2007, and 53 percent of them were diagnosed or suspected to be from lymphoma.

The research warned there was a high prevalence of the disease in the colony and it was evident that a virus (STLV-1) may be playing a role in the increasing spread of the disease.

It concluded that management of the baboons needed to take into account the transmission of the disease by preventing sexual contact between positive and negative animals. It also said it was the first published report about the presence of the STLV-1 virus in non-human primates in Australia.

The research on babies at the facility revealed that 16 baby baboons were killed over a 12-year period from 1994-2006 at the Wallacia facility. Almost all were from trauma related injuries, although two deaths were undetermined due to a lack of records and the body of another was too decomposed to determine the cause of death. One baby went missing and the body was never found.

The research, which was looking at the survival rate of babies born to first-time and multiple-birth mothers, found there had been 146 pregnancies during a twelve-year period and of those 106 were born alive and 40 were stillborn or aborted.

Of those, the researchers said, at least three abortions and six stillbirths were directly related to experiments being carried out on their mothers for pregnancy-related diseases. Another four stillbirths were suspected to have been caused by the experiments. The research concluded the breeding program was a success because of the low rate of pregnancy loss, high survival rate and lack of maternal mortality.