Four of the buildings have facades which are protected in the district plan.
The resource consent granting the right to demolish the buildings came despite the area being a protected townscape precinct, and despite both the council's consultant architect and its planner arguing that the facade of 386 Princes St, at least, should have been saved.
The buildings will be replaced by versions with facades closely resembling the originals.
Trust Otago-Southland area manager Owen Graham said the decision had the potential to "impact significantly on the historic character of this area of the city".
"Unfortunately, in this case council opted not to uphold its protected heritage listing for this group of four historic buildings, which comprises some of Dunedin's earliest built heritage dating to the 1860s," Mr Graham said.
A considerable number of people, including those who had signed a petition handed to the council, were opposed to the decision.
The trust was reviewing the contents of the decision before considering its options.
There is a 15-day appeal period.
Mr Graham said the Canterbury earthquake, and public response to the loss of so many heritage places, showed "widespread recognition of how important historic places are to New Zealanders".
"There's a profound understanding that once gone they cannot be brought back," he said.
The majority decision to allow the demolition of 372-392 Princes St, and 11 Stafford St, and replace them with a development of 15 apartments with space for retailing on the ground floor, came from a hearings committee of Crs Colin Weatherall, Richard Walls and Fliss Butcher.
It followed an interim decision in February that the committee was "of a mind" to grant consent if Christchurch-based developer Luke Dirkzwager, came up with a design more representative of the precinct's character.
