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It disputed claims by council chief executive Clare Hadley who stressed the restructure was not a response to Covid-19.
In a submission to the council, leaked to the Otago Daily Times, PSA organiser Jon Henning said the pandemic was a "significant factor in driving the increased number of roles the council is now proposing to disestablish".
Staff were concerned about the future effectiveness of a local government organisation "that they care deeply about".
Feedback from union members included questions about job losses, including those that had already occurred and those roles not being replaced.
The submission said this "substantially increased pressures on remaining staff".
Outsourcing of work and delays around performance were also highlighted.
"We are concerned that the present direction and culture of the organisation may be associated with a high turnover of staff."
In the statement, Mr Henning said the proposal would result in the permanent elimination of some roles.
He believed it was a practice by those in central and local government, who were keen to minimise public services, to outsource work to private enterprise.
"This is almost always an ideological and destructive choice."
The letter concluded questioning the restructure proposal’s authors’ understanding of the organisation.
Mr Henning confirmed yesterday he wrote the submission but was unable to comment further.
The council proposal said while some jobs would be axed, 13 would be established.
According to the council document, the purpose of the restructure was to address key issues identified by the council’s leadership team and the need for "a greater sense of urgency in the way we perform our activities".
A final decision is expected on Friday and any changes will be implemented next month.