From next week the NT government will stop charging rent for public housing based on income and introduce a bedroom-based scheme.
The scheme will apply throughout remote communities, in the Alice Springs town camps and in Tennant Creek community living areas.
Rents will be set at $70 per bedroom, per week but capped at $280 a week.
The NT government believes the changes will make paying rent easier to understand, cut rental debt and provide a fairer public housing system.
But Aboriginal Housing NT chief executive Skye Thompson said they would result in two-thirds of tenants being hit with a rent increase and lead to more people heading into Alice Springs looking for a place to live.
"Raising the rents of the most marginalised people in the Northern Territory will only put further pressure on families, especially around central Australia," Ms Thompson said.
"We're concerned that the framework will compound cost-of-living pressures, and could see even more people in remote communities move into towns like Alice Springs.
"The framework will put more pressure on people who are already overwhelmingly living below the poverty line."
Ms Thompson said in light of those pressures, the NT government should maintain the current income-based rent model until a new system could be designed in partnership with stakeholders.
She said Aboriginal Housing NT was concerned the government was pushing ahead with the change without having properly modelled its impact on tenants and communities.
It also comes after last week's move to restrict alcohol sales in central Australia in a bid to curb surging youth crime in Alice Springs.
The restrictions include a three-month ban on the sale of takeaway alcohol in the region on Mondays and Tuesdays and reduced trading hours on other days, with a limit of one purchase per person each day.
A long-term central Australian alcohol management plan will also be developed.
