The 2016 Australian Annual Surveillance report into sexually transmissible infections and blood-borne viruses was released by the University of New South Wales' Kirby Institute on Monday.
The research found that while cases of HIV have stabilised overall in Australia, reported cases in Indigenous men have doubled over the past five years, and are now two times higher than non-Indigenous men.
The report also found the rates of infection with chlamydia and gonorrhoea in Indigenous Australians continue to increase, despite advances in treatment and medical services.
But the story is different when it comes to non-indigenous Australians, as the rate of HIV remains stable.
Associate Professor James Ward, head of Infectious Diseases Research Program - Aboriginal Health at the South Australian Health and Medical Research Institute, told the ABC treatment and prevention of HIV for Australia's wider population hasn't reached remote areas.
"These test and treat strategies probably haven't filtered into the primary healthcare providers for Aboriginal people which are predominantly Aboriginal medical services. I think we need to put a real lot of effort into ensuring that test and treat strategies are rolled out," he says.
But there is some good news on genital warts, down 91 per cent in Aboriginal and Torres Strait Islander women aged under 21. This is similar to the decline seen in the non-Indigenous population of the same age, thanks to HPV vaccination programs in schools.