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"Many businesses are still getting back on their feet after lockdown, and this is a considerable setback," association chief executive Virginia Nicholls said.
Many offices in Otago were already sending staff home to work, Mrs Nicholls said.
"... right now at Alert Level 2 we need these businesses to continue working from their offices - and supporting these local businesses including cafes and retailers."
Otago Chamber of Commerce chief executive Dougal McGowan also had heard of offices sending people home to work.
It was vital people here got on to the tracing app and used it diligently, he said.
"That could be the difference between Level 2, Level 3 or Level 4.
"That’s going to mean the traceability is going to be a whole lot easier."
The lockdown of Aucklanders would trickle down negatively on the wider economy.
Queenstown Chamber of Commerce executive chairman Craig Douglas said the uncertainty of the Covid-19 cases in Auckland hit "our shores pretty quickly".
He had heard of "plenty" of cancellations by yesterday morning and expected Air New Zealand’s schedule to change drastically today.
He was concerned Queenstown businesses did not have the reserves to get them through another lockdown scenario.
"... there’s going to have to be something [in terms of further financial support].