Around £21m will be needed to implement the changes to the benefit system, which will affect around 32,000 homes.
Figures released by two housing organisations show that the proposed new tax will leave a £4m shortfall, as it is predicted the tax will cut the benefits bill by £17m.
The NI Federation of Housing Associations (NIFHA) and the Chartered Institute of Housing (CIHNI) are now calling for the proposals to be dropped in the region.
The organisations estimate that housing association tenants will lose close to £4m in housing benefit in the first year that the Bedroom Tax is implemented.
It is likely to cost the Housing Executive at least £10m a year, and the reassessment of housing benefit will add a further £500,000 to the bill.
Cameron Watt, Chief Executive of NIFHA said reforms are necessary, but described the Bedroom Tax as an "ill-conceived policy".
"It will hurt vulnerable people in Northern Ireland, causing financial hardship for tens of thousands of families," he said.
"It's clear that the numbers don't add up on Bedroom Tax. Northern Ireland can't afford the human or economic damage this policy would inflict."
CIH NI Director Cecilia Keaveney added: "These figures confirm what housing professionals have long suspected - introducing the Bedroom Tax in Northern Ireland just doesn't add up.
"It will cause real hardship for some of the most vulnerable members of our society as well as posing huge challenges for social landlords, particularly given the unique profile of social housing here.
"We've always known that there would be a significant human cost to the bedroom tax, but these figures show that there is also considerable financial cost to the sector and Northern Ireland Executive."
The Welfare Reform Bill will be discussed at the Assembly later this month, when MLAs will have the opportunity to debate Bedroom Tax.
This research, while welcome, produces a figure of cost which I would suggest is a conservative one.
Mark H Durkan, SDLP
Mark H Durkan, the SDLP's Social Development spokesman, has welcomed the research.
He claims that the estimated cost of implementing the tax is too conservative.
"I want to praise NIFHA and CIH for the research they have conducted. The figures produced confirm what the SDLP have been saying, that the cost of imposing bedroom tax greatly outweighs any savings that may be made," he said.
"Our party has been continuously admonished by others for suggesting that the bedroom tax was unworkable. They have hidden behind a false premise that this tax will bring real savings and today's figures disprove that entirely."
The Foyle MLA added: "The money allocated for Discretionary Housing Payments should also be factored into this cost.
"Hopefully other political parties will take heed of this research and join with the SDLP to block the implementation of this invidious bedroom tax which will hit up to 32,000 across Northern Ireland."
Judith Cochrane, Alliance's East Belfast MLA, is calling on the Social Development Minister Nelson McCausland - and the Executive - to adopt a common sense approach on the issue.
"While many aspects of welfare reform have the potential to assist and empower people to move into employment and where appropriate to reduce their dependency on social security, a number of aspects are deeply controversial and counterproductive," she said.
"The 'bedroom tax' is perhaps the most offensive aspect of the so-called reforms. Fundamentally, it is a dehumanising measure, which doesn't adequately take into account personal circumstances the need for flexibility.
"There is now a strong case for the Minister for Social Development, the Executive and the Assembly adopting a Northern Ireland approach on this aspect of welfare reform, and to make a final case to Westminster for flexibility in this regard, and to consider all other options as to how common sense can prevail locally."