Dunstan's scanner will be installed immediately, while Queenstown will get its machine later.
The need for another scanner for patients in the wider Central Otago and Queenstown Lakes area was raised by a National Health Board panel, but there has been much debate since on where it should be located.
The panel recommended the scanner be installed at Lakes District Hospital but Central Otago Health Services Ltd, (COHSL), which runs Dunstan Hospital, had been lobbying for several years to have a scanner there.
At yesterday's SDHB meeting, chairman Joe Butterfield praised staff for coming up with a workable plan in less than a year. There had been "tensions up west" about the location, he said.
"It looks like we have a solution which will work for both communities."
The board endorsed a mixed funding model comprising board money, private provider money and community support.
Total capital, operational and depreciation funding for the two sites would be $5 million for the first seven years, with the board providing $2.2 million, a private investor $1.4 million and $1.4 million coming from the communities, funding and finance general manager Robert Mackway-Jones told the district health board earlier.
Including depreciation in the budget would allow the scanners to be replaced at the end of their lives in about seven years' time.
On Wednesday, the board announced a review of radiology services throughout its region as part of efforts to reduce waiting times for tests, including scans.
Responding to a question yesterday, Mr Mackway-Jones said he was comfortable about going ahead with the dual scanner plans given the wider review.
Providing one, and later two, scanners would address "equity of access" issues, and have an economic benefit for the Central Otago and Queenstown-Lakes area, as fewer people would have to travel for scans.
Based on SDHB data for the past two years, about 1300 Queenstown-Lakes and Central Otago people had publicly-funded scans annually. That figure was expected to rise to 1700 each year, which would bring the number of scans per head of population to about the same level as the rest of Otago.
It was also expected about 300 ACC scans could be done in Clyde and/or Queenstown each year.
Board member Richard Thomson asked yesterday whether scans would be read by SDHB staff or staff from private companies. There was already a private radiology company contracted to provide some services at Dunstan Hospital, he said.
Mr Mackway-Jones said the detail still had to be worked through but the board would look at the capacity within its own radiology department first, with a "fall-back position" of talking to a private provider.
"Doing it ourselves" was generally cheaper, he said.
Board member Dr Malcolm Macpherson withdrew from the debate. He is a member of the Central Lakes Trust, which he said was a potential scanner funder.