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The developer of the site that once housed the Scribes shop and accommodation units in Great King St may also have breached rules about disturbing archaeology.
The history of the buildings dates back to the 19th century.
Developer Tony Tan, of Dayniel Ltd, had obtained a demolition consent, but complications came to light last week.
The Building Act allowed exemptions to the need for a building consent, including for some types of demolition, but this applied only to standalone buildings, a Dunedin City Council spokesman said.
The site has a party wall with an adjoining building.
Council staff had contacted representatives of the site owner and the demolition company working there and they agreed to stop work until the building consent issue had been resolved, the spokesman said.
Heritage New Zealand Otago-Southland office spokesman Frank van der Heijden said the developer needed to have gained permission to fully demolish pre-1900 buildings or to disturb any sub-surface archaeology.
This had not been obtained, he said.
Mr Tan said the party wall requires a separate consent to be demolished, so we are waiting for it before we continue.
The plan detailed in consent documents involved creating another commercial premises, 10 accommodation units and parking.
This would be complemented by a communal roof-top garden.
The masonry-clad building at the corner of Great King and St David Sts was most likely constructed in the late 19th century, a heritage report states.
It was used for both commercial and residential purposes and its occupants included an umbrella manufacturer, a piano teacher and furnishing shop.
The second-hand bookshop Scribes had been there since the early 1990s.
Mr Tan said last week he bought the site soon after lockdown last year.
It turned out to be in poor shape and he said he had little choice but to proceed with demolition.