Chamber chief executive John Christie said the case of Dean Mason, who wanted to rebuild after a fire at his Birch St site, was being watched closely.
It was believed to be the first time the impact of the Dunedin City Council's harbourside plan change had been felt by an industrial business within the new harbourside zone.
There was also "immediate concern" for several other businesses in the area, with business owners in talks with the council about what they could, or could not do under the new harbourside rules, Mr Christie said.
There were believed to be 100 existing businesses, providing "hundreds" of jobs, in the area covered by the plan change, which was adopted in mid-2008 to encourage the development of cafes, restaurants and apartments in the area.
The chamber remained concerned a lack of suitable alternative industrial land in Dunedin meant the plan change would force businesses, and jobs, out of the city, he said.
"We are obviously concerned there's an impact already being felt on businesses as a result of the plan change.
"We are certainly concerned at the moment that access to the harbour by this plan change will cost the city jobs."
Earlier this week, Mr Mason told the Otago Daily Times he had approached council staff hoping to build a 13,000sq m industrial building on the site of the former Japanese Auto Wreckers Ltd on Birch St, Dunedin.
His original building was destroyed in a suspicious fire at the site in early May this year, forcing the Japanese Auto Wreckers business to relocate to another site in Dunedin.
Mr Mason said plans for the new building had been prepared, and a potential tenant had expressed interest, but council staff this week raised doubts the building would be allowed under "existing use" rules.
Those rules allowed Mr Mason up to one year to begin replacing the destroyed building with a new one of the same type, but council staff have indicated they were "yet to be convinced" the proposed new building complied with existing use requirements.
If it did not, the new harbourside rules - which were now believed to have more weighting than overlapping district plan rules for the area - meant Mr Mason would be required to apply for a resource consent.
The new rules, shifting the emphasis away from industrial development in the area, meant his application was also more likely to face hurdles at a resource consent hearing, council planning policy manager Paul Freeland indicated this week.
Mr Christie said Mr Mason's situation was an example of the kind of problem that prompted the chamber's submission to the council's annual plan hearings in May, calling for the plan change to be halted while further consultation was undertaken.
The chamber and five businesses have also launched an Environment Court challenge to the plan change, which led to mediation talks between the chamber, businesses and council staff.
Yesterday, Mr Christie said the mediation process was continuing, but in the meantime Mr Mason appeared to be "in a very difficult position".
"It's not going to get any easier for businesses. The outcome for him is going to be a real acid test, or litmus test, for anyone else."
