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The section, in Castle St, is part of the land sold late last year by Cadbury owner Mondelez to the Government.
The car park and former factory site were bought for $11.6million, and will eventually become part of the new Dunedin Hospital project.
An SDHB spokesman said the organisation was managing the former car park on behalf of the Crown.
"As part of this arrangement, we have allocated a number of marked parking spaces for Southern DHB pool cars, Ministry of Health vehicles and other specified vehicles," he said.
"We are exploring options for how the remainder of the parks might be managed for use by SDHB staff."