The community-run pool is in the Fraser Building, opposite the main hospital, and it has been in limbo because of uncertainty about the rebuild.
A planned upgrade has been postponed indefinitely.
Southern District Health Board chief executive Chris Fleming said there would be discussions with the pool trust in the coming months.
The rebuild business case document reveals the Government wants to sell the hospital campus after the new hospital is built in 2027.
The campus includes the Fraser building.
Some people had hoped the new hospital would be built in the Fraser building block, between Hanover and Frederick Sts, as construction there would not affect clinical activity in the main hospital.
The block is partly owned by the University of Otago, which had indicated it wanted to work with the Government to allow the development.
It is understood the Ministry of Health ruled that out, as it did not want to compensate the university for the cost of replacing its halls of residence.
Otago Therapeutic Pool Trust secretary-treasurer Neville Martin said the pool's fate would not be known until decisions were made about the possible sale of the site.
``If it is to be sold, will the new owner grant a long-term lease for the same purpose?
``I doubt that a buyer seeking a commercial return on the investment would be interested in buying the site on that basis,'' Mr Martin said.
Senior doctors' union spokesman John Chambers said he expected to hear little new information about the rebuild for some time.
``The whole matter of the Dunedin Hospital rebuild will not now be the subject of any real development until after the new Government have settled in, and given the matter some thought, which will be after Christmas [and the] silly season,'' Dr Chambers said.
The Government has promised to try to find a new central city spot, but if it is unable to do so, the main hospital would be rebuilt at Wakari Hospital.
