It has been affected by an international problem - proficient pipe organists slowly ageing and retiring, with few young people taking their places.
The cathedral had been "rather lucky up to now" to have replacement organists waiting in the wings, its choirmaster, Michael McConnell, said.
In recent years, John Barker had been succeeded by his son-in-law, Kemp English, who taught his replacement, Rachel Swindells.
Ms Swindells (23) finished on Sunday to spend more time on her postgraduate music studies at the University of Otago.
She will still play at Dunedin's Anglican cathedral, St Paul's, when principal organist David Burchall is unavailable and will remain the organist at Knox College chapel.
Mr McConnell said he could not contemplate the cathedral without an organist.
"If no organist is forthcoming it will be a challenging time for the choir. We will be doing tons of unaccompanied singing and more Gregorian chants.
"At non-choir Masses and when the music group is not assisting, let's hope the parish priest is in good voice to lead the congregation."
Ms Swindells, who last month won New Zealand's major performance prize for organists, said there were many reasons why young people were not attracted to learning to play the pipe organ, including its lack of portability and its complexity.
The St Joseph's organ has three keyboards, 180 keys, 71 stops, or combination levers, and more than 30 pedals, which require precise co-ordination between hands, feet and eyes.
"It is remarkably similar to driving a car," she said yesterday.
Another reason was the "unexciting" music young people generally heard being played on a pipe organ.
"There is a repertoire of innovative and exciting music available for organ and young people need to be exposed to that.
"It is crisis time. We have to entice young people to play the organ or it [the skill] will die."
Mr McConnell said another difficulty in attracting an organist was money.
While an honorarium was paid, it was not a living wage.
However, he hoped the cathedral vacancy would attract a musician to Dunedin.
"The job [with us] wouldn't be enough in itself, but it could be a deciding factor for someone who was already thinking of moving to Dunedin or studying at the university."
