The Railway Street drugs misuse service in Ballymena was partly paid for by the Department of Justice.
However, it is withdrawing funding after 14 years due to budget cuts.
The service has been independently assessed as a model of best practice in helping injecting drug users across the UK.
Justice Minister David Ford said the move was "regrettable but unavoidable".
"It is one of many difficult funding decisions I am currently having to make in order to balance the books," he said.
"In light of the financial constraints being imposed I have advised the Northern Trust that the Department of Justice share of the funding for this partnership project between the justice system and the health service would cease on 28 February 2015."
Oscar Donnelly, director of mental health and disability for the Northern Trust, said: "Unfortunately the withdrawal of two thirds of the funding for the scheme means that we will not be able to sustain it in its present form.
"The trust will need to review the way in which a significantly reduced service can be provided in the future."
A facility in County Antrim that works to reduce the harm caused by drugs will close early next year because of a lack of funding.