She feared in a significant earthquake the building would "collapse out onto the street and kill and injure pedestrians".
The retailer reported seeing pink brick dust covering the inside of the building after the Kaikoura earthquake in November 2016.
Cordoning off the building was a last resort, infrastructure and sustainability portfolio leader councillor Iona Pannett said.
"We consistently work hard with owners to find solutions when a building is prone but that has been difficult in this case."
She said the Wellington City Council had powers under the Building Act to take over the building and strengthen it, then bill the owner.
Pannett said she would like to see the heritage-listed building saved.