An Indigenous health program which has been running in Queensland for 21 years is set to close this year when federal funding stops.
The federal health department gave the Queensland AIDS Council a 12-month funding extension to keep the 2 Spirits sexual health program operating.
During that time, the department expected the council to "explore more sustainable funding alternatives".
But the council was told in a letter on Monday no further funding would be available after June 30.
"The department thanks your organisation and staff for the valuable contribution you have made to providing health care activities through your service delivery activities to Aboriginal and Torres Strait Islander people," the federal health department said in the letter obtained by AAP.
The council fears the cut comes at a time when more work is needed to prevent Indigenous sexually transmitted diseases and promote better sexual health practices, particularly among gay and lesbian people.
Council director Michael Scott told AAP sexually transmitted disease infection rates were up to 20 times higher among Indigenous people than non-Indigenous people.
One of the main projects which would be affected by the cut was the distribution of medication for HIV prevention.
Mr Scott said one of the biggest challenges was Indigenous LGBTI people did not go to local Aboriginal medical services because of the stigma attached to being LGBTI.
"What we've found is building trust and rapport over time is what is needed," Mr Scott said.
"The time is right for a comprehensive investment in Indigenous health."
The 2 Spirits program was responsible for one of the most recognisable health promotion programs in Australia, Condoman, which sought to promote and encourage condom use.
A national study in 2015 found between 2012-2014, the notification rate of new HIV diagnosis in the Aboriginal and Torres Strait Islander population (5.9 per 100,000) was higher than in the non-Indigenous population (3.7 per 100,000).
Chlamydia notification rates in the Indigenous population have been around three times higher than the rate in the non-Indigenous population, while gonorrhoea notifications are 18 times higher than in the non-Indigenous population and the figure for infectious syphilis is four times higher.
Labor frontbencher Terri Butler told AAP on Tuesday she was greatly concerned by the cut.
"Now is not the time to be axing a program aimed at sexual health in Indigenous communities," she said.
Comment was being sought from federal Indigenous health minister Ken Wyatt.
Another program, run by the Northern Territory AIDS and Hepatitis Council, has also had its federal funding cancelled from June 30.
The council was also asked to explore "more sustainable funding alternatives" over the past 12 months, before being told of the funding cut.
The department of health said the Commonwealth was still funding primary care, including care for sexually transmitted infections and blood borne viruses.
It had given the Queensland AIDS Council around $400,000 a year for sexual heath activities, but decided to discontinue the funding after a review in 2015.
"The AIDS Council has been aware that since 2015 they would only get funding up to 30 June 2017 and was advised to make alternative arrangements," a department spokeswoman said in a statement.
"Sexual and reproductive health is primarily a state and territory responsibility."
