A member of the Port Chalmers Fishermen's Co-operative was involved in discussions with community stakeholders over widening the reserve to include the whole harbour.
"It appears something was lost in translation because we do not support a mataitai covering the entire harbour," said president Steve Little.
Initially, the reserve area was to be for a smaller area in front of the Otakou marae, but a decision was reached to include the whole harbour, with several exclusion areas for port activities.
The co-operative, which represents 26 commercial fishermen from Timaru to Bluff, believes a mataitai is not "in the best interest of the whole harbour".
"But we support a sustainable fishery," he said.
Despite no commercial fishing activities taking place in Otago Harbour for "30 or 40 years", Mr Little said the co-operative supported commercial fishing of cockles from the harbour.
Southern Clams, which is represented in the co-operative, had applied to the Ministry of Fisheries for a special permit to investigate cockle harvesting in the harbour.
That application may be in jeopardy because a reserve excludes commercial fishing from its area, although it can be permitted.
"Southern Clams are actively trying to open up an opportunity. It is a nonsense to close it [the proposed reserve] off to prevent all those opportunities and jobs," Mr Little said.
Te Runanga o Otakou project manager Hoani Langsbury said he was surprised to hear of the co-operative's change of direction.
"We spoke to the co-op' and they were happy with the proposal."
Mr Langsbury said the runanga was waiting to hear from the Ministry of Fisheries regarding the application, before it was publicly notified.
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