A study into microcephaly, where babies are born with smaller heads, found foetal alcohol spectrum disorder and genetic conditions can cause the birth defect.

The birth defect microcephaly had the world's attention when images of Zika-infected babies spread around the globe, and a study of abnormal births in Western Australia has now linked the condition to two other causes.

Microcephaly, where a baby is born with a smaller than normal head, is also caused by foetal alcohol spectrum disorder (FASD) and genetic disorders, the study found.

The research, published in the Medical Journal of Australia, found there were 478 cases of the birth defect documented on the West Australian Register of Developmental Anomalies from 1980 to 2015.

Researchers analysed these births, finding on average there were five cases of microcephaly per 10,000 births, with annual rates ranging between 2.9 per cent and 7.7 per cent.

A cause for microcephaly was only established in 45 per cent of cases, more frequently for Aboriginal births (70 per cent) than non-Aboriginal births (38 per cent).

FASD, a neurodevelopmental disorder caused when an unborn child is exposed to alcohol in the womb, is the most frequent cause of microcephaly in Aboriginal children.

The disorder also causes trouble with cognitive abilities such as planning, language skills, reading, gross motor skills and memory.

Chromosomal defects and monogenic disorders, such as Down syndrome and cystic fibrosis, were the main causes of microcephaly in non-Aboriginal babies.

The joint study by the Telethon Kids Institute, King Edward Memorial Hospital and the WA Department of Health was prompted by the World Health Organisation recommending countries at risk of Zika virus transmission gather baseline data on the disorder.

The WA Health Department says while the Zika virus hasn't been reported in Australia, there is an ongoing risk of the Zika-spreading Aedes aegypti mosquito returning to the state.

The Aedes aegypti mosquito is found in northern and central Queensland and the department warns infected travellers returning to Australia could infect these mosquitoes and cause an outbreak.

Brazil declared an end to its public health emergency over Zika last Thursday, but the WHO has warned the virus is "here to stay," even when cases of it fall off.