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Landowners at the site of the planned new hospital between Cumberland and Castle Sts say they have recently received notice their land is required under the Public Works Act.
The former Cadbury site sold by Mondelez appears to be the only site sold so far.
The $1.4billion project is expected to begin in 2020, with work ending in 2026.
Drilling has been under way in Cumberland St this week as geotechnical work is undertaken.
The Otago Daily Times understands the Wilson Parking site on the corner of St Andrew St and Cumberland St is not yet sold, and Aurora Energy said recently its site on the same block had yet to be sold.
Otago Land Group Ltd's Martin Dippie said the process of buying the land was ''very technical''.
''We only got served the formal notice last week.''
His land is between Cumberland and Castle Sts, by Hanover St, and has VTNZ and Wilson Parking as tenants.
Mr Dippie said the hospital was ''fantastic for the city'' but it was unfortunate it was on land for which he had development plans.
He explained that he had been a long way down a path of what he described as an exciting development for Dunedin.
However he said: ''We're very positive about the process, and very respectful of it.''
Ian Hamilton of Cumberland Commercial Holdings Ltd owns land further south, with Warehouse Stationery, Anytime Fitness and Lighting Direct as tenants.
Mr Hamilton said he too had only recently received notice of the process.
''It's very early in the process.''
Another land owner also told the Otago Daily Times he had only recently received notice his land was required.
The Ministry of Health has engaged The Property Group to negotiate the sale.
The process includes a three-month period of discussion and valuation, in which owners decide whether or not they accept the price offered to them.
If agreements are unable to be reached, it generally takes between six to 12 months to compulsorily acquire land.
However landowners can go the the Environment Court in a case where their land is compulsorily acquired.