The Queensland AIDS Council’s 2 Spirits program is set to close after losing federal funding.

The Department of Health had given the council a 12-month funding extension to keep the Indigenous sexual health program operating.

The council was told on Monday no funding would be available after 30 June.

“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 a letter to the Queensland AIDS Council.

Staff fear the cut will be to the detriment of work needed to prevent STIs and promote better sexual health practices for Indigenous Australians, particularly gay and lesbian people.

Director Michael Scott said STI rates are up to 20 times higher among Indigenous people.

Scott said one of the biggest challenges is indigenous LGBTI people often do 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,” he said.

“The time is right for a comprehensive investment in Indigenous health.”

One of the main projects that will be affected by the funding cut is distribution of HIV prevention medication.

The Queensland AIDS Council was responsible for the creation of Condoman, one of the most recognised recent public health campaigns, which aims to normalise and promote condom use for Indigenous people.

Labor frontbencher Terri Butler said 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.

The Northern Territory AIDS and Hepatitis Council has also had its federal program funding cut from 30 June.

Both councils were asked to find “more sustainable funding alternatives” over the past year, before being told of the funding cut this week.

The Department of Health said the federal government is still funding primary health care, including treatment for STIs and blood borne viruses.

“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,” said a department spokesperson.

“Sexual and reproductive health is primarily a state and territory responsibility.”

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