Replacing the shelters is part of the development in the central city and temporary structures will be used to provide cover in the meantime.
A six-storey building could open late next year in Great King St next to Farmers and it is to be a "flagship branch" for Pacific Radiology.
Asked how the bus hub might be affected, the Otago Regional Council said the construction management plan provided for the hub to operate as normal during construction.
Existing shelters to be removed would be used in other parts of the city, council transport manager Lorraine Cheyne said.
They would quickly be replaced by units not unlike shipping containers, or gantry-type shelters, dropped into place by crane.
"They provide shelter from weather and protection from any construction debris," Ms Cheyne said.
"There will be shelters in place throughout construction."
The frontage of the building is expected to be completed about October next year, which is when permanent new shelters would be put in place.
Asked if the developer would pick up the cost, Ms Cheyne said construction of the canopy was a component of the site development.
