It is believed that thousands of Australian women are on the therapy, which is an unbranded, unregulated form of standard HRT supplied by some pharmacists and online.
It is promoted as a more "natural'' form of HRT, used widely to treat the symptoms of menopause like hot flashes and night sweats.
Hot flashes are typically experienced as a feeling of intense heat with sweating and rapid heartbeat, and may typically last from two to thirty minutes for each occurrence. The event may be repeated a few times each week or constantly throughout the day, with the frequency reducing over time.
Biomedical HRT has been suspected of being linked to cancer but this study, published in the latest Medical Journal of Australia, is the first proof of a clinical pattern.
Dr John Eden, associate professor of reproductive endocrinology at the University of New South Wales, and his co-authors, said that taking estrogen was known to increase risk of endometrial carcinoma, cancer of the endometrium (uterus lining).
For this reason, standard HRT approved by the Therapeutic Goods Administration contains a careful counterbalance of progestin, a synthetic form of progesterone, known to lower the risk.
Progesterone is one of the hormones in women that stimulate and regulate various functions. Progesterone plays a role in maintaining pregnancy. The hormone is produced in the ovaries, the placenta (when a woman gets pregnant) and the adrenal glands. It helps prepare the body for conception and pregnancy and regulates the monthly menstrual cycle. It also plays a role in sexual desire.
Dr.Eden suggested the cases of the three NSW women - two who were menopausal and one who was still getting periods - raised the possibility that bioidentical HRT increased the risk of developing cancer as a result of high levels of oestrogen.
"It should be noted that the Australasian Menopause Society does not recommend the use of bioidentical HRT,'' Dr Eden said.
"Until this therapy has been properly tested, it may be prudent not to advocate bioidentical HRT, and to perform annual ultrasounds and biopsies on women who continue to use this therapy''.
Sydney reproductive health specialist Professor Michael Chapman said bioidentical HRT was promoted by many pharmacists and specialists who believed the doses, taken either as a lozenge or as a cream that is rubbed in, were more appropriate than standard HRT.
"These women take what they believe are the right hormones at right doses but that's not necessarily the case,'' Prof Chapman said.
"The hormones are bought from the same sources as drug companies but the difference is the stringency for testing is huge.''
He warned women off the treatment, saying it was "crazy for people to endanger themselves like this when there is a range of much safer and tested products on the market''.