The six-storey building, which houses 450 council staff, a public service centre and iSite, moved in the earthquake but did not suffer any obvious serious structural damage.
Staff who usually work in the building are either using other council buildings or working from home.
The BNZ Harbour Quays building will be closed for months, while Farmers Cuba St, Deloitte House and Wellington High Court are among a number of buildings still waiting on assessments before re-opening.
The Customhouse Quay building will be out of action for months
Meanwhile, a 110 tonne excavator should start demolishing the city's most affected building in Molesworth St this week.
Wellington City Council manager of building compliance and consents Mike Scott said the nine-storey building will be demolished from the top down.
Jaw-like machinery will crunch the building down, in what he said was a relatively quiet process.
The building was built in the 1960s and asbestos had been discovered by contractors, which made the deconstruction more complicated.
Part of the cordon on Molesworth St could be lifted as soon as next week.
The Ministry of Business, Innovation and Employment's Tenancy Compliance Investigation team is investigating whether the building was being illegally used for residential accommodation.
Wellington mayor Justin Lester said he was aware of three residential tenancies in the building at the time, which has prompted Wellington MP Grant Robertson to ask what happened to the rent money the family were paying.