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Central Lakes Trust chief executive Paul Allison said the trust's working conditions were less than ideal, with no meeting space and staff having to share offices.
Dr Greg White, of Cromwell Medical, said the centre was cramped and beyond its capacity.
General practitioners had been using a portable building as an extra consulting room.
"We will be getting more rooms and more space for visiting specialists. We will be able to get more allied health professionals in," he said.
Work is progressing on the two-storey building, which is owned by the Central Otago District Council.
Once the two entities move in, ownership will transfer to the trust.
It will occupy some of the second floor and lease the remainder.
The medical centre will move into the ground floor.
Mr Allison said they had spent considerable time looking for the right location.
"Because of the location, we will be seen as part of the mall. We wanted to be in it to make sure any activity won't negatively impact the mall."
Building started late last year and is expected to be finished by August.