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But the closure is actually good news for the 148-year-old church.
The congregation is moving to First Church for three months while a $100,000 upgrade takes place.
The project would include the installation of a new sprinkler system, cleaning of the roof and church organ and repairs to the south-facing stained glass window, lifelong church member David Hill said.
The church had to close as "it would be covered in scaffolding to reach the 20m ceiling", he said.
"It wasn't possible to run a service so the decision to move to First Church was the best decision."
Funds for the work would largely be provided by the synod, with the parish raising the rest through grants and fund-raising, he said.
The church already had a partial fire sprinkler system and the installation of a complete system would help reduce the insurance bill, which was now $15,000 per year.
On taking down the organ's pipes, Mr Hill said "they had more dust than Mt Vesuvius."
The congregation at First Church was expected to swell to more than 200 while Knox was closed, Knox minister Rev Dr Sarah Mitchell said.
She would alternate Sunday services with Rev Tokerau Joseph from First Church, and once a month they would together hold a joint service.
The office and community centre at Knox Church will remain open.