The NI Housing Executive (NIHE) could be abolished in five years under government plans to reduce bureaucracy.
Peter Hain made the announcement about quangos
The number of unelected quangos and public bodies in Northern Ireland are being drastically cut.
The final stage of the Review of Public Administration will see the number of such bodies in Northern Ireland almost halved from 154 to 75.
The NIHE is to lose some functions to seven super councils in 2009, and it could disappear altogether by 2011.
Chief Executive of the Northern Ireland Housing Executive, Paddy McIntyre, said the timing of the transfer of housing functions was a matter for ministers.
"The statement says until the new functions are transferred, till the new councils are working, till they are operational and bedded down suggests to me that it's not going to be five years because those councils don't come into affect until 2009," he said.
"We are still there, as confirmed by the secretary of state, discharging a significant portfolio of functions."
Last November, Northern Ireland Secretary Peter Hain announced the first part of the Review of Public Administration reducing 26 district councils to seven and cutting the number of education and health boards.
This latest cull of quangos means the eventual demise of bodies such as Enterprise Ulster and the Housing Council, while other bodies will merge.
The changes announced in Belfast by Northern Ireland Secretary Peter Hain on Tuesday are likely to save less than £20m.
However, Mr Hain said they would "cut costs and transfer resources from bureaucracy to frontline delivery of key public services like health and education".
Key changes will mean:
- There will be a new Land and Property Agency which will incorporate valuation and lands, rate collection, land registers and Ordnance Survey agencies
- A Library Authority will be created with responsibility for all libraries across Northern Ireland
- Driver and Vehicle Licensing will merge with the Driver and Vehicle Testing Agency
- The Northern Ireland Events Company will become part of the Northern Ireland Tourist Board
- Some of the funding currently administered by the Arts and Sports Councils will become the responsibility of local government, as will some of the functions of the NITB and Invest NI
- The Public Records Office will transfer to central government
- The Northern Ireland Housing Council, the Agriculture Wages Board and Enterprise Ulster will cease to exist
In practice, Mr Hain said, the new system would mean fewer public bodies, with wider remits and the ability to deliver better co-ordination of services.
"We believe that housing is essentially a local issue and for that reason we will consider the transfer of housing to local government at a future date, once the new councils are in place, fully operational and bedded in," he said.
"In the meantime, however, while the Northern Ireland Housing Executive will remain, some of its non-core functions will transfer to local government when the new councils are established in 2009."
In future, appointments to public bodies will be made on merit through the public appointments procedure.
However, the seven new councils will now have 60 councillors each, rather than 50 as earlier envisaged.
BBC Northern Ireland political correspondent Gareth Gordon said this was possibly a concession to most of the political parties - apart from Sinn Fein - who wanted 15 councils to remain.
He said the future of the Housing Executive would prove "the most controversial".
"It will lose a sixth of its annual budget of £600m and 300 of its 3,000 staff... to the new councils when they are set up in 2009," he said.
In a statement, the Northern Ireland Housing Executive said: "The Secretary of State's announcement acknowledges the political sensitivities that still exist around housing.
"We agree with the analysis that housing functions should only be considered for transfer once the new councils have bedded in.
"The new arrangements need to protect the progress that has been made in delivering fair housing."