The federal government decided to stop funding two long-running Indigenous sexual health programs without consultation or analysis, and despite a growing sexual health crisis in the Top End, Senate estimates has heard.

Both organisations have accused the government of shortsightedness, and said without their services, or any feasible replacement, Indigenous LGBTQI people will be less likely to seek medical care.

The Northern Territory Aids and Hepatitis Council’s Aboriginal sexual health program, and the Queensland Aids Council’s 2 Spirits program have run for more than 20 years addressing the disproportionately high rate of sexually transmitted infections among Aboriginal and Torres Strait Islander populations.

Both organisations were told last year they should seek alternative funding to continue operating beyond June 2017.

In Senate estimates last week, Department of Health officials said they had done a “desktop review” of programs. The review found “really limited evidence that these programs, which we’ve been funding for decades now, have really had any impact”, according to Bobbi Campbell, the first assistant secretary at the department.

Asked if the department had asked the NT and Queensland programs to partner with the department for an evaluation, Campbell said no. “We need to look at this from national perspective.”

The Queensland Aids Council’s executive director, Michael Scott, said his organisation had more than two decades of experience and community rapport, and its annual funding of $451,000 was a “drop in the ocean” for the work they did.

“We employ four Indigenous staff and they work from a whole-of-community approach, which means even though we’re funded to work with Indigenous gay men and sistagirls, we do remote outreach to Indigenous remote populations, to the entire community,” he said.

“It is a really important service because we also do training for other organisations, such as Aboriginal medical services, on how to appropriately work with Indigenous gay men and sistagirls.”

During the estimates hearing department officials also pointed to the rising rates of STIs and HIV in Indigenous populations, particularly the remote communities where the two organisations work. While the rate of new cases of HIV among non-Indigenous men and women stabilised in the four years to 2015, the rate among Indigenous men doubled.

Aboriginal and Torres Strait Islander men were twice as likely to have HIV than non-Indigenous men, according to the University of New South Wales Kirby institute for infection and immunity in society, which also reported rates of chlamydia, gonorrhoea and syphilis were, respectively, three, 10, and six times greater than among the non-Indigenous population in 2015. Remote and very remote areas saw even more substantial differences.

Last year the number of syphilis cases in the NT increased to 229 from just 14 in 2012. The high rate is set to continue in 2017, with more cases reported in January than for the whole of 2012.

Scott said his employees had been told people in the community would probably not seek care elsewhere once 2 Spirits closed.

“They forgo health care because they’re not comfortable walking through the door,” he said. “They’ll be living with STIs because they aren’t getting tested. That’s not just a health issue for them but for their communities as well.”

Daniel Alderman, a care and support coordinator for the Northern Territory Aids and Hepatitis Council, said his organisation had heard similar reports.

“This directly affects the most marginalised population we work with, Indigenous clients, [who] as you know suffer significant trauma,” he told Guardian Australia.

“Then we have seen more marginalised communities – sistagirls, brotherboys … they’re shunned from their communities that they live in and suffer significant stigma and discrimination.

“It’s cutting funding to Indigenous employment and one of the common things we hear from our Indigenous clients is they don’t want to access general or Aboriginal medical services because they fear they’ll be discriminated against.”

The Labor MP Warren Snowdon said the government didn’t just fail to perform an evaluation but “ignored the fact that these organisations had been operating for 21 years and providing an important service”.

“It beggars belief they can be canning these programs without any transition to other programs and leaving exposed these people who are involved [to] sexually transmitted infections and Aids,” he told Guardian Australia.

He said the cost of prevention far outweighed the cost of treating someone with HIV, and accused the government of “wiping its hands” of the responsibility.

“You’re prepared to pay for the treatment of HIV … but you’re not prepared to pay upfront for the prevention programs,” he said. “It doesn’t make sense.”

A spokeswoman for the department of health said funding for primary care, including for STIs and blood-borne viruses, continued along with prevention and education work.

“Since July 2014, funding to the AIDS Council has been on a year to year basis. Following a review of these activities in 2015 the commonwealth advised the AIDS Council that funding would not be continued,” she said.

Sexual and reproductive health was primarily a state and territory responsibility, she said.